Profiling Gene Expression from GSE and TCGA

Before begin, it’s recommended to read these publications:

We will make similar results like these : Example 1 Example 2

This is my results for FAM86A : FAM86A

Normal vs Tumor from Gene Expression Omnibus

Install and load libraries:

Sys.setenv(LANG='en') #change warning to English 
Sys.setenv("VROOM_CONNECTION_SIZE" = 131072 * 10) #prevent connection lost when roaming big chunk
library(GEOquery)
library(limma)
library(tidyverse)
library(dplyr)
library("ggsci")
library(rstatix)

To make graph look nice and consistents, I make my own function :

####Aziz' function's theme and color palettes

scale_fill_aziz <- function(...){
  library(scales)
  discrete_scale("fill","aziz",manual_pal(values = c("#386cb0","#fdb462","#7fc97f","#a6cee3","#fb9a99","#984ea3","#ffff33")), ...)
  
}
scale_colour_aziz <- function(...){
  library(scales)
  discrete_scale("colour","aziz",manual_pal(values = c("#386cb0","#fdb462","#7fc97f","#ef3b2c","#662506","#a6cee3","#fb9a99","#984ea3","#ffff33")), ...)
} 
theme_Publication <- function(base_size=14, base_family="helvetica") {
  library(grid)
  library(ggthemes)
  (theme_foundation(base_size=base_size, base_family=base_family)
    + theme(plot.title = element_text(face = "bold",
                                      size = rel(1.2), hjust = 0.5),
            text = element_text(),
            panel.background = element_rect(colour = NA),
            plot.background = element_rect(colour = NA),
            panel.border = element_rect(colour = NA),
            axis.title = element_text(face = "bold",size = rel(1)),
            axis.title.y = element_text(angle=90,vjust =2),
            axis.title.x = element_text(vjust = -0.2),
            axis.text = element_text(), 
            axis.line = element_line(colour="black"),
            axis.ticks = element_line(),
            panel.grid.major = element_line(colour="#f0f0f0"),
            panel.grid.minor = element_blank(),
            legend.key = element_rect(colour = NA),
            legend.position = "bottom",
            legend.direction = "horizontal",
            legend.key.size= unit(0.2, "cm"),
            legend.margin = unit(0, "cm"),
            legend.title = element_text(face="italic"),
            plot.margin=unit(c(10,5,5,5),"mm"),
            strip.background=element_rect(colour="#f0f0f0",fill="#f0f0f0"),
            strip.text = element_text(face="bold")
    ))
  
}
#### GSE62254 (ACRG)
gset <- getGEO("GSE66229", GSEMatrix =TRUE, AnnotGPL=TRUE)
if (length(gset) > 1) idx <- grep("GPL570", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

# make proper column names to match toptable 
fvarLabels(gset) <- make.names(fvarLabels(gset))

# group membership for all samples
gsms <- paste0("11100000000000000111110000000000000000100111111111",
               "11111111111111111111111111111111111111111111111111",
               "11111111111111111111111111111111111111111111111111",
               "11111111111111111111111010111101111000000111111111",
               "11111111111111111111111111111111111111111111111111",
               "11111111111111111111111111111111111111111111111111",
               "11111111111111111111111111111111111100000111110000",
               "00000000000000000000000000000000000000000000000000")
sml <- strsplit(gsms, split="")[[1]]

# log2 transformation
ex <- exprs(gset)
qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
LogC <- (qx[5] > 100) ||
  (qx[6]-qx[1] > 50 && qx[2] > 0)
if (LogC) { ex[which(ex <= 0)] <- NaN
exprs(gset) <- log2(ex) }

# assign samples to groups and set up design matrix
gs <- factor(sml)
groups <- make.names(c("N","T"))
levels(gs) <- groups
gset$group <- gs
design <- model.matrix(~group + 0, gset)
colnames(design) <- levels(gs)

fit <- lmFit(gset, design)  # fit linear model

# set up contrasts of interest and recalculate model coefficients
cts <- paste(groups[1], groups[2], sep="-")
cont.matrix <- makeContrasts(contrasts=cts, levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)

# compute statistics and table of top significant genes
fit2 <- eBayes(fit2, 0.01)
tT <- topTable(fit2, adjust="fdr", sort.by="B", number=250)

tT <- subset(tT, select=c("ID","adj.P.Val","P.Value","t","B","logFC","Gene.symbol","Gene.title"))


# Visualize and quality control test results.
# Build histogram of P-values for all genes. Normal test
# assumption is that most genes are not differentially expressed.
tT2 <- topTable(fit2, adjust="fdr", sort.by="B", number=Inf)
hist(tT2$adj.P.Val, col = "grey", border = "white", xlab = "P-adj",
     ylab = "Number of genes", main = "P-adj value distribution")

#prepare for only genes passing the threshold
newtT2<-tT2 %>% 
  filter(adj.P.Val<0.05)

newtT3 <- subset(newtT2,select=c("ID","adj.P.Val","t","B","logFC","Gene.symbol","Gene.title"))
write.csv(newtT3,file="normal tumor acrg fdr ok genes.csv") #you can check the directory

#retrieve the expression of your gene in all patient
threegenes<-ex[row.names(ex) %in% c("219617_at", #camkmt
                                    "222013_x_at", #FAM86A
                                    "206445_s_at"),] #PRMT1
write.csv(threegenes,file="acrg cmt fam prmt1.csv")

# download phenotypes
my.gse <- "GSE66229"

if(!file.exists("geo_downloads")) dir.create("geo_downloads")
if(!file.exists("results"))  dir.create("results", recursive=TRUE)
my.geo.gse <- getGEO(GEO=my.gse, filename=NULL, destdir="./geo_downloads", GSElimits=NULL, GSEMatrix=TRUE, AnnotGPL=FALSE, getGPL=FALSE)
my.geo.gse <- my.geo.gse[[1]]
my.pdata <- as.data.frame(pData(my.geo.gse), stringsAsFactors=F)
write.csv(my.pdata,file="phenotype acrg.csv")
#assign Expression data with phenotype in excel (efficient using vlookup formula) : format like below

nt<-read.csv('graph nt acrg.csv',sep='\t')
head(nt)
##           ID    PRMT1   CAMKMT   FAM86A Tissue
## 1 GSM1523727 2.957375 1.999631 1.758549      T
## 2 GSM1523728 3.128566 1.689934 1.830104      T
## 3 GSM1523729 3.052887 1.806846 1.791574      T
## 4 GSM1523730 2.916911 1.659223 1.750806      N
## 5 GSM1523731 2.789613 1.710085 1.744396      N
## 6 GSM1523732 3.088736 1.715045 1.766945      N
acrg<-nt
acrg<-acrg %>% 
  mutate(Tissue2 = case_when(Tissue == 'N' ~ 'Normal',
                             Tissue == 'T' ~ 'Tumor'))
acrg$Tissue2 <- factor(acrg$Tissue2, levels = c("Normal", "Tumor"))
GSEacrg<-ggplot(acrg,aes(x=Tissue2,y=FAM86A,fill=Tissue2))+

  labs(y=expression('FAM86A expression (log'[10]*")"),x=NULL)+
  
  stat_boxplot(geom ='errorbar',width=.2) +
  geom_jitter(colour='gray90',alpha=.8,width = .2)+
  geom_boxplot(width=.6)+
  theme_Publication()+
  scale_fill_aziz()+
  scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
  theme(axis.text.x = element_text(),
        legend.position = 'none',
        axis.title.x = element_blank(),
        panel.grid.major.x = element_blank(),
        aspect.ratio = 1.85)

GSEacrg

#statistical analysis
wilcox.test(FAM86A ~ Tissue2, data = acrg,
            exact = FALSE)
## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  FAM86A by Tissue2
## W = 11848, p-value = 0.001646
## alternative hypothesis: true location shift is not equal to 0
acrg %>% wilcox_effsize(FAM86A ~ Tissue2)
## # A tibble: 1 x 7
##   .y.    group1 group2 effsize    n1    n2 magnitude
## * <chr>  <chr>  <chr>    <dbl> <int> <int> <ord>    
## 1 FAM86A Normal Tumor    0.157   100   300 small
gset <- getGEO("GSE54129", GSEMatrix =TRUE, AnnotGPL=TRUE)
if (length(gset) > 1) idx <- grep("GPL570", attr(gset, "names")) else idx <- 1
gset <- gset[[idx]]

# make proper column names to match toptable 
fvarLabels(gset) <- make.names(fvarLabels(gset))

# group membership for all samples
gsms <- paste0("00000000000000000000011111111111111111111111111111",
               "11111111111111111111111111111111111111111111111111",
               "11111111111111111111111111111111")
sml <- strsplit(gsms, split="")[[1]]

# log2 transformation
ex <- exprs(gset)
qx <- as.numeric(quantile(ex, c(0., 0.25, 0.5, 0.75, 0.99, 1.0), na.rm=T))
LogC <- (qx[5] > 100) ||
  (qx[6]-qx[1] > 50 && qx[2] > 0)
if (LogC) { ex[which(ex <= 0)] <- NaN
exprs(gset) <- log2(ex) }

# assign samples to groups and set up design matrix
gs <- factor(sml)
groups <- make.names(c("N","T"))
levels(gs) <- groups
gset$group <- gs
design <- model.matrix(~group + 0, gset)
colnames(design) <- levels(gs)

fit <- lmFit(gset, design)  # fit linear model

# set up contrasts of interest and recalculate model coefficients
cts <- paste(groups[1], groups[2], sep="-")
cont.matrix <- makeContrasts(contrasts=cts, levels=design)
fit2 <- contrasts.fit(fit, cont.matrix)

# compute statistics and table of top significant genes
fit2 <- eBayes(fit2, 0.01)
tT <- topTable(fit2, adjust="fdr", sort.by="B", number=250)

tT <- subset(tT, select=c("ID","adj.P.Val","P.Value","t","B","logFC","Gene.symbol","Gene.title"))

# Visualize and quality control test results.
# Build histogram of P-values for all genes. Normal test
# assumption is that most genes are not differentially expressed.
tT2 <- topTable(fit2, adjust="fdr", sort.by="B", number=Inf)
hist(tT2$adj.P.Val, col = "grey", border = "white", xlab = "P-adj",
     ylab = "Number of genes", main = "P-adj value distribution")

# summarize test results as "up", "down" or "not expressed"
dT <- decideTests(fit2, adjust.method="fdr", p.value=0.05)

# Venn diagram of results
vennDiagram(dT, circle.col=palette())

#our code start
newtT2<-tT2 %>% 
  filter(adj.P.Val<0.05)

newtT3 <- subset(newtT2,select=c("ID","adj.P.Val","t","B","logFC","Gene.symbol","Gene.title"))
write.csv(newtT3,file="normal tumor GSE54129 fdr ok genes.csv")


####################expression of selected genes############
threegenes<-ex[row.names(ex) %in% c("219617_at", #camkmt
                                    "222013_x_at", #FAM86A
                                    "206445_s_at"),]#PRMT1
write.csv(threegenes,file="GSE54129 cmt fam prmt1.csv")



#####################phenotypes
my.gse <- "GSE54129"

if(!file.exists("geo_downloads")) dir.create("geo_downloads")
if(!file.exists("results"))  dir.create("results", recursive=TRUE)
my.geo.gse <- getGEO(GEO=my.gse, filename=NULL, destdir="./geo_downloads", GSElimits=NULL, GSEMatrix=TRUE, AnnotGPL=FALSE, getGPL=FALSE)
my.geo.gse <- my.geo.gse[[1]]
my.pdata <- as.data.frame(pData(my.geo.gse), stringsAsFactors=F)
write.csv(my.pdata,file="phenotype GSE54129.csv")

#plot
G129<-read.csv('graph nt GSE54129.csv',sep='\t')
head(G129)
##           ID    PRMT1   CAMKMT   FAM86A Tissue
## 1 GSM1308392 9.452179 6.115939 6.425237      N
## 2 GSM1308393 9.443866 5.661901 6.131955      N
## 3 GSM1308394 8.921622 5.910835 6.128566      N
## 4 GSM1308395 8.664146 5.537663 6.460649      N
## 5 GSM1308396 8.938331 5.695038 6.163880      N
## 6 GSM1308397 9.011761 5.955174 6.169497      N
G129<-G129 %>% 
  mutate(Tissue2 = case_when(Tissue == 'N' ~ 'Normal',
                             Tissue == 'T' ~ 'Tumor'))

G129$Tissue2 <- factor(G129$Tissue2, levels = c("Normal", "Tumor"))
GSE4129<-ggplot(G129,aes(x=Tissue2,y=FAM86A,fill=Tissue2))+
  labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)+
  
  stat_boxplot(geom ='errorbar',width=.2) +
  geom_jitter(colour='gray90',alpha=.8,width = .2)+
  geom_boxplot(width=.6)+
  theme_Publication()+
  scale_fill_aziz()+
  scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
  theme(axis.text.x = element_text(),
        legend.position = 'none',
        axis.title.x = element_blank(),
        panel.grid.major.x = element_blank(),
        aspect.ratio = 1.85)

GSE4129

#statistical analysis
wilcox.test(FAM86A ~ Tissue2, data = G129,
            exact = FALSE)
## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  FAM86A by Tissue2
## W = 475, p-value = 1.764e-05
## alternative hypothesis: true location shift is not equal to 0
G129 %>% wilcox_effsize(FAM86A ~ Tissue2)
## # A tibble: 1 x 7
##   .y.    group1 group2 effsize    n1    n2 magnitude
## * <chr>  <chr>  <chr>    <dbl> <int> <int> <ord>    
## 1 FAM86A Normal Tumor    0.374    21   111 moderate

Unify GTEx NAT and Tumor TCGA

stomach.rsem.fpkm.gtex <- read.delim("~/stomach-rsem-fpkm-gtex.txt")
stad.rsem.fpkm.tcga.t <- read.delim("~/stad-rsem-fpkm-tcga-t.txt")
stad.rsem.fpkm.tcga <- read.delim("~/stad-rsem-fpkm-tcga.txt")

df.gtex<-stomach.rsem.fpkm.gtex
df.t.tcga<-stad.rsem.fpkm.tcga.t
df.n.tcga<-stad.rsem.fpkm.tcga


library(tidyverse)
library(dplyr)
Sys.setenv(LANG='en')

############GTEx###############
colnames(df.gtex)
##   [1] "Hugo_Symbol"                    "Entrez_Gene_Id"                
##   [3] "GTEX.QCQG.0526.SM.48U2A"        "GTEX.QDVJ.1426.SM.48U1Y"       
##   [5] "GTEX.13111.1226.SM.5GCNC"       "GTEX.S4Z8.1226.SM.4AD6W"       
##   [7] "GTEX.ZDYS.1926.SM.5HL59"        "GTEX.144GM.1726.SM.5O9AS"      
##   [9] "GTEX.PWOO.1226.SM.48TCO"        "GTEX.146FR.2026.SM.5NQAI"      
##  [11] "GTEX.1399R.1126.SM.5IFIO"       "GTEX.WHWD.1426.SM.4OORU"       
##  [13] "GTEX.111CU.0926.SM.5EGIK"       "GTEX.WZTO.2126.SM.4PQYW"       
##  [15] "GTEX.T8EM.1226.SM.4DM5J"        "GTEX.NFK9.1526.SM.3LK7B"       
##  [17] "GTEX.YEC4.1426.SM.5IFHS"        "GTEX.T5JC.1926.SM.4DM6Q"       
##  [19] "GTEX.WFG8.1326.SM.4LVN3"        "GTEX.OXRK.1626.SM.3NB17"       
##  [21] "GTEX.P4PQ.1526.SM.3NMCK"        "GTEX.ZA64.0826.SM.5HL9U"       
##  [23] "GTEX.1399S.1626.SM.5P9GI"       "GTEX.R55C.1026.SM.48FCM"       
##  [25] "GTEX.P4PP.1526.SM.3P61M"        "GTEX.13OVI.2426.SM.5KM4J"      
##  [27] "GTEX.146FH.2126.SM.5SI9U"       "GTEX.145ME.1026.SM.5O9B4"      
##  [29] "GTEX.13113.0726.SM.5LZUF"       "GTEX.13X6H.1626.SM.5Q5CT"      
##  [31] "GTEX.13O3Q.2126.SM.5KM4C"       "GTEX.WHPG.0426.SM.4M1XW"       
##  [33] "GTEX.Y8E4.1526.SM.4WWDI"        "GTEX.ZE7O.3026.SM.51MS4"       
##  [35] "GTEX.VJYA.1026.SM.4KL21"        "GTEX.S4Q7.0726.SM.4AD5F"       
##  [37] "GTEX.U8T8.1226.SM.4E3IH"        "GTEX.Y114.1226.SM.4TT88"       
##  [39] "GTEX.1211K.1426.SM.5FQTF"       "GTEX.RM2N.0826.SM.48FD3"       
##  [41] "GTEX.12696.1726.SM.5EQLH"       "GTEX.12WSG.2026.SM.5FQUU"      
##  [43] "GTEX.OOBJ.1526.SM.3NB1Q"        "GTEX.PX3G.1526.SM.48U11"       
##  [45] "GTEX.WFON.1126.SM.4LVMA"        "GTEX.11P82.0726.SM.5PNYL"      
##  [47] "GTEX.QV31.0626.SM.447C5"        "GTEX.R55G.1126.SM.48FDG"       
##  [49] "GTEX.14BMU.1126.SM.5RQJ8"       "GTEX.SIU7.1426.SM.4BRWT"       
##  [51] "GTEX.Q2AH.1126.SM.48TZM"        "GTEX.13OW6.2526.SM.5IJEC"      
##  [53] "GTEX.13O61.1126.SM.5L3FI"       "GTEX.XBEW.1826.SM.4RTWX"       
##  [55] "GTEX.S341.0626.SM.4AD5T"        "GTEX.ZT9W.1526.SM.4YCDE"       
##  [57] "GTEX.13QJ3.2726.SM.5SI6L"       "GTEX.RU1J.0526.SM.46MUT"       
##  [59] "GTEX.XAJ8.0326.SM.47JYI"        "GTEX.PW2O.1226.SM.48TCH"       
##  [61] "GTEX.12WSK.1426.SM.5CVNN"       "GTEX.SNOS.0826.SM.4DM5N"       
##  [63] "GTEX.YEC3.1426.101806.SM.5PNXX" "GTEX.11VI4.0326.SM.5EQ6L"      
##  [65] "GTEX.132AR.2426.SM.5IFFD"       "GTEX.W5WG.1726.SM.4LMI5"       
##  [67] "GTEX.Y5LM.1326.SM.5RQIS"        "GTEX.PWCY.0926.SM.48TD7"       
##  [69] "GTEX.ZVT2.1626.SM.51MRC"        "GTEX.S3XE.1026.SM.4AD4O"       
##  [71] "GTEX.13D11.2126.SM.5IFH2"       "GTEX.XUZC.0726.SM.4BOPH"       
##  [73] "GTEX.QMRM.1126.SM.447BN"        "GTEX.XBED.1226.SM.4AT5V"       
##  [75] "GTEX.X15G.1126.SM.4PQZG"        "GTEX.Q734.1026.SM.48U16"       
##  [77] "GTEX.1399U.1626.SM.5P9J3"       "GTEX.RWS6.0926.SM.47JXE"       
##  [79] "GTEX.TKQ2.0926.SM.4DXU5"        "GTEX.12C56.0526.SM.5FQST"      
##  [81] "GTEX.145LT.1426.SM.5O9B3"       "GTEX.S4P3.0726.SM.4AD57"       
##  [83] "GTEX.13FTX.0726.SM.5N9BI"       "GTEX.ZLV1.0826.SM.4WWEQ"       
##  [85] "GTEX.11NUK.2426.SM.5BC4U"       "GTEX.ZVP2.1626.SM.5GU5D"       
##  [87] "GTEX.ZF2S.1426.SM.57WET"        "GTEX.12WSD.2326.SM.59HKQ"      
##  [89] "GTEX.U3ZN.2026.SM.4DXUC"        "GTEX.133LE.1326.SM.5IFGO"      
##  [91] "GTEX.1122O.1926.SM.5EGIQ"       "GTEX.11TT1.0726.SM.5GU5A"      
##  [93] "GTEX.R53T.1226.SM.48FCT"        "GTEX.ZAB4.1526.SM.5CVN7"       
##  [95] "GTEX.11EQ9.1226.SM.5987E"       "GTEX.144GN.1226.SM.5O991"      
##  [97] "GTEX.145MN.1326.SM.5NQ9S"       "GTEX.1339X.1426.SM.5K7YO"      
##  [99] "GTEX.Y9LG.1026.SM.5IFJN"        "GTEX.ZQUD.0826.SM.57WDQ"       
## [101] "GTEX.13U4I.2526.SM.5SI8Z"       "GTEX.OHPK.1526.SM.3MJGM"       
## [103] "GTEX.P4QT.1526.SM.3NMCT"        "GTEX.QLQ7.0826.SM.447B3"       
## [105] "GTEX.ZXES.1426.SM.5NQ8S"        "GTEX.RTLS.2626.SM.46MUJ"       
## [107] "GTEX.QV44.1226.SM.4R1KE"        "GTEX.YJ8A.1526.SM.5P9FT"       
## [109] "GTEX.13PVQ.2126.SM.5L3FW"       "GTEX.TMMY.1626.SM.4DXTY"       
## [111] "GTEX.ZTX8.0426.SM.59HLG"        "GTEX.14BMV.2226.SM.5RQHX"      
## [113] "GTEX.XV7Q.1326.SM.4BRWM"        "GTEX.145MO.2226.SM.5Q5BN"      
## [115] "GTEX.QXCU.1926.SM.48FE4"        "GTEX.117YW.2226.SM.5N9DB"      
## [117] "GTEX.13FTW.1726.SM.5KM2B"       "GTEX.ZV6S.0926.SM.57WGB"       
## [119] "GTEX.WH7G.1526.SM.4LVMX"        "GTEX.XQ8I.2026.SM.4BOOL"       
## [121] "GTEX.YFCO.0826.SM.5LUAG"        "GTEX.SNMC.0626.SM.4DM6H"       
## [123] "GTEX.UPIC.1826.SM.4IHKC"        "GTEX.ZVZP.1726.SM.5GZWY"       
## [125] "GTEX.ZZPU.1426.SM.5GZZ6"        "GTEX.139D8.2326.SM.5IFGE"      
## [127] "GTEX.139YR.1926.SM.5LZXM"       "GTEX.T6MO.0726.SM.4DM58"       
## [129] "GTEX.11I78.1726.SM.5A5M3"       "GTEX.T5JW.0926.SM.4DM5K"       
## [131] "GTEX.Y5V6.1326.SM.4VDTF"        "GTEX.111YS.1126.SM.5GZYQ"      
## [133] "GTEX.S95S.0826.SM.4B64N"        "GTEX.13S7M.1826.SM.5RQK6"      
## [135] "GTEX.UJHI.1026.SM.4IHJP"        "GTEX.11GSP.2126.SM.5HL5E"      
## [137] "GTEX.13O21.0926.SM.5IFGT"       "GTEX.12BJ1.1726.SM.5HL9B"      
## [139] "GTEX.117YX.1026.SM.5H11V"       "GTEX.11NSD.1426.SM.5HL67"      
## [141] "GTEX.12WSJ.0926.SM.5P9JD"       "GTEX.13QBU.1126.SM.5LU44"      
## [143] "GTEX.ZY6K.0726.SM.5A5L8"        "GTEX.V955.1326.SM.4JBHR"       
## [145] "GTEX.ZYVF.2726.SM.5GID4"        "GTEX.POMQ.0826.SM.3P61H"       
## [147] "GTEX.WFG7.1326.SM.4LMK1"        "GTEX.QLQW.0726.SM.447AA"       
## [149] "GTEX.XUJ4.1226.SM.4BOPD"        "GTEX.11DXX.1326.SM.5GIDZ"      
## [151] "GTEX.ZPIC.2026.SM.57WG3"        "GTEX.Y3IK.1426.SM.4YCES"       
## [153] "GTEX.ZYY3.1726.SM.5EGH3"        "GTEX.PLZ6.0826.SM.3P61K"       
## [155] "GTEX.QDVN.1226.SM.48TZ5"        "GTEX.OIZH.1526.SM.3NB1J"       
## [157] "GTEX.13N1W.2026.SM.5K7YU"       "GTEX.131XF.1226.SM.5HL8V"      
## [159] "GTEX.13CF3.1926.SM.5K7WF"       "GTEX.11EM3.1026.SM.5A5KL"      
## [161] "GTEX.13FH7.1026.SM.5IJGF"       "GTEX.UPK5.2126.SM.4JBJK"       
## [163] "GTEX.Y8LW.0826.SM.4WWDO"        "GTEX.ZZ64.0426.SM.5E43F"       
## [165] "GTEX.ZLFU.1326.SM.4WWET"        "GTEX.UJMC.1226.SM.4IHLI"       
## [167] "GTEX.131XE.2226.SM.5PNYX"       "GTEX.R55D.1526.SM.48FEJ"       
## [169] "GTEX.S4UY.1626.SM.4AD55"        "GTEX.O5YW.1526.SM.3MJGL"       
## [171] "GTEX.V1D1.1726.SM.4JBHB"        "GTEX.ZYFG.1326.SM.5GICJ"       
## [173] "GTEX.ZVT3.2126.SM.59HL2"        "GTEX.XXEK.0826.SM.4BRWG"       
## [175] "GTEX.Y3I4.1626.SM.4TT7W"        "GTEX.WEY5.1226.SM.4LMIQ"       
## [177] "GTEX.PWN1.1526.SM.48TDA"        "GTEX.Q2AI.0826.SM.48TZO"       
## [179] "GTEX.TKQ1.0526.SM.4DXTG"        "GTEX.11WQK.2626.SM.5EQ4K"      
## [181] "GTEX.WFJO.1126.SM.4LVLZ"        "GTEX.11P7K.1726.SM.5GU6F"      
## [183] "GTEX.U4B1.1026.SM.4DXT1"        "GTEX.WRHK.0626.SM.4MVOE"       
## [185] "GTEX.13RTK.0226.SM.5RQHR"       "GTEX.11EI6.2426.SM.5PNVS"      
## [187] "GTEX.P78B.1826.SM.3P5YX"        "GTEX.S7SF.0626.SM.4AD4V"       
## [189] "GTEX.XPVG.1526.SM.4B66C"        "GTEX.132QS.1826.SM.5IFFN"      
## [191] "GTEX.ZPU1.1626.SM.4WWB2"        "GTEX.ZP4G.1226.SM.4WWCJ"       
## [193] "GTEX.131XG.1226.SM.5EGH9"       "GTEX.ZV7C.1626.SM.5NQ7E"
df.gtex.FAM86A<-df.gtex %>% 
  filter(Hugo_Symbol == 'FAM86A')

head(df.gtex.FAM86A)[2]
##   Entrez_Gene_Id
## 1         196483
dim(df.gtex.FAM86A)
## [1]   1 194
#transposing
df.gtex.FAM86A<-df.gtex.FAM86A %>% 
  gather(Patients,FPKM,3:ncol(.))

dim(df.gtex.FAM86A)
## [1] 192   4
head(df.gtex.FAM86A)
##   Hugo_Symbol Entrez_Gene_Id                 Patients   FPKM
## 1      FAM86A         196483  GTEX.QCQG.0526.SM.48U2A 224.97
## 2      FAM86A         196483  GTEX.QDVJ.1426.SM.48U1Y 220.32
## 3      FAM86A         196483 GTEX.13111.1226.SM.5GCNC 121.79
## 4      FAM86A         196483  GTEX.S4Z8.1226.SM.4AD6W 185.11
## 5      FAM86A         196483  GTEX.ZDYS.1926.SM.5HL59 171.45
## 6      FAM86A         196483 GTEX.144GM.1726.SM.5O9AS 185.11
df.gtex.FAM86A.log2<-df.gtex.FAM86A %>% 
  mutate(log2FPKM=log(FPKM,base = 2))
head(df.gtex.FAM86A.log2)
##   Hugo_Symbol Entrez_Gene_Id                 Patients   FPKM log2FPKM
## 1      FAM86A         196483  GTEX.QCQG.0526.SM.48U2A 224.97 7.813589
## 2      FAM86A         196483  GTEX.QDVJ.1426.SM.48U1Y 220.32 7.783457
## 3      FAM86A         196483 GTEX.13111.1226.SM.5GCNC 121.79 6.928252
## 4      FAM86A         196483  GTEX.S4Z8.1226.SM.4AD6W 185.11 7.532239
## 5      FAM86A         196483  GTEX.ZDYS.1926.SM.5HL59 171.45 7.421644
## 6      FAM86A         196483 GTEX.144GM.1726.SM.5O9AS 185.11 7.532239
#######NAT###########
colnames(df.n.tcga)
##  [1] "Hugo_Symbol"                  "Entrez_Gene_Id"              
##  [3] "TCGA.BR.6564.11A.01R.1884.13" "TCGA.HU.A4GH.11A.11R.A36D.31"
##  [5] "TCGA.IN.8663.11A.01R.2402.13" "TCGA.HU.8238.11A.01R.2343.13"
##  [7] "TCGA.BR.7716.11A.01R.2055.13" "TCGA.FP.7735.11A.01R.2055.13"
##  [9] "TCGA.HU.A4GY.11A.11R.A36D.31" "TCGA.IN.AB1X.11A.21R.A39E.31"
## [11] "TCGA.CG.5720.11A.01R.1602.13" "TCGA.IN.8462.11A.01R.2343.13"
## [13] "TCGA.BR.7704.11A.01R.2055.13" "TCGA.CG.5722.11A.02R.1602.13"
## [15] "TCGA.BR.6458.11A.01R.1802.13" "TCGA.HU.A4HB.11A.11R.A251.31"
## [17] "TCGA.CG.5734.11A.01R.1602.13" "TCGA.IN.AB1V.11A.11R.A414.31"
## [19] "TCGA.FP.7829.11A.01R.2055.13" "TCGA.BR.6453.11A.01R.1802.13"
## [21] "TCGA.BR.6457.11A.01R.1802.13" "TCGA.IP.7968.11A.01R.2203.13"
## [23] "TCGA.HU.A4GN.11A.12R.A251.31" "TCGA.HU.A4GP.11A.21R.A251.31"
## [25] "TCGA.CG.5730.11A.01R.1602.13" "TCGA.IN.7806.11A.01R.2055.13"
## [27] "TCGA.BR.6454.11A.01R.1802.13" "TCGA.BR.7715.11A.01R.2055.13"
## [29] "TCGA.CG.5733.11A.01R.1602.13" "TCGA.BR.6852.11A.01R.1884.13"
## [31] "TCGA.BR.6802.11A.01R.1884.13" "TCGA.HU.A4G3.11A.11R.A24K.31"
## [33] "TCGA.BR.7851.11A.01R.2203.13" "TCGA.CG.5721.11A.01R.1602.13"
## [35] "TCGA.BR.7717.11A.01R.2055.13"
df.n.tcga.FAM86A<-df.n.tcga %>% 
  filter(Hugo_Symbol == 'FAM86A')

head(df.n.tcga.FAM86A)[2]
##   Entrez_Gene_Id
## 1         196483
dim(df.n.tcga.FAM86A)
## [1]  1 35
#transposing
df.n.tcga.FAM86A<-df.n.tcga.FAM86A %>% 
  gather(Patients,FPKM,3:ncol(.))

dim(df.n.tcga.FAM86A)
## [1] 33  4
head(df.n.tcga.FAM86A)
##   Hugo_Symbol Entrez_Gene_Id                     Patients   FPKM
## 1      FAM86A         196483 TCGA.BR.6564.11A.01R.1884.13 220.32
## 2      FAM86A         196483 TCGA.HU.A4GH.11A.11R.A36D.31 202.66
## 3      FAM86A         196483 TCGA.IN.8663.11A.01R.2402.13 166.73
## 4      FAM86A         196483 TCGA.HU.8238.11A.01R.2343.13 163.28
## 5      FAM86A         196483 TCGA.BR.7716.11A.01R.2055.13 249.73
## 6      FAM86A         196483 TCGA.FP.7735.11A.01R.2055.13 256.78
df.n.tcga.FAM86A.log2<-df.n.tcga.FAM86A %>% 
  mutate(log2FPKM=log(FPKM,base = 2))
head(df.n.tcga.FAM86A.log2)
##   Hugo_Symbol Entrez_Gene_Id                     Patients   FPKM log2FPKM
## 1      FAM86A         196483 TCGA.BR.6564.11A.01R.1884.13 220.32 7.783457
## 2      FAM86A         196483 TCGA.HU.A4GH.11A.11R.A36D.31 202.66 7.662918
## 3      FAM86A         196483 TCGA.IN.8663.11A.01R.2402.13 166.73 7.381370
## 4      FAM86A         196483 TCGA.HU.8238.11A.01R.2343.13 163.28 7.351204
## 5      FAM86A         196483 TCGA.BR.7716.11A.01R.2055.13 249.73 7.964225
## 6      FAM86A         196483 TCGA.FP.7735.11A.01R.2055.13 256.78 8.004389
#######Tumor###########
colnames(df.t.tcga)
##   [1] "Hugo_Symbol"                  "Entrez_Gene_Id"              
##   [3] "TCGA.BR.6457.01A.21R.1802.13" "TCGA.VQ.A8PD.01A.11R.A414.31"
##   [5] "TCGA.BR.6803.01A.11R.1884.13" "TCGA.VQ.A8E3.01A.11R.A39E.31"
##   [7] "TCGA.CG.5718.01A.11R.1602.13" "TCGA.VQ.A8E2.01A.11R.A36D.31"
##   [9] "TCGA.CD.5799.01A.11R.1602.13" "TCGA.BR.6452.01A.12R.1802.13"
##  [11] "TCGA.CG.4438.01A.01R.1157.13" "TCGA.BR.4257.01A.01R.1131.13"
##  [13] "TCGA.CD.A48C.01A.11R.A24K.31" "TCGA.D7.5577.01A.01R.1602.13"
##  [15] "TCGA.BR.A4IV.01A.31R.A251.31" "TCGA.FP.8631.01A.11R.2402.13"
##  [17] "TCGA.BR.A452.01A.91R.A251.31" "TCGA.BR.4187.01A.01R.1131.13"
##  [19] "TCGA.BR.6706.01A.11R.1884.13" "TCGA.CD.5803.01A.11R.1602.13"
##  [21] "TCGA.VQ.AA6B.01A.11R.A414.31" "TCGA.BR.8295.01A.11R.2343.13"
##  [23] "TCGA.BR.8059.01A.11R.2343.13" "TCGA.CG.5724.01A.11R.1602.13"
##  [25] "TCGA.F1.6177.01A.11R.1802.13" "TCGA.HU.A4GH.01A.11R.A24K.31"
##  [27] "TCGA.HU.8608.01A.11R.2402.13" "TCGA.BR.6456.01A.11R.1802.13"
##  [29] "TCGA.BR.A4IZ.01A.32R.A251.31" "TCGA.BR.A4PF.01A.11R.A251.31"
##  [31] "TCGA.RD.A8N5.01A.12R.A36D.31" "TCGA.HU.8610.01A.22R.2402.13"
##  [33] "TCGA.HU.A4GQ.01A.11R.A36D.31" "TCGA.HU.A4HD.01A.11R.A251.31"
##  [35] "TCGA.HU.A4HB.01A.12R.A251.31" "TCGA.VQ.A925.01A.11R.A414.31"
##  [37] "TCGA.BR.6852.01A.11R.1884.13" "TCGA.BR.4292.01A.01R.1131.13"
##  [39] "TCGA.BR.6705.01A.12R.1884.13" "TCGA.BR.A4J5.01A.21R.A251.31"
##  [41] "TCGA.BR.6709.01A.11R.1884.13" "TCGA.MX.A666.01A.11R.A31P.31"
##  [43] "TCGA.BR.A4QI.01A.12R.A251.31" "TCGA.BR.7959.01A.11R.2343.13"
##  [45] "TCGA.D7.8576.01A.11R.2343.13" "TCGA.VQ.A8E0.01A.11R.A414.31"
##  [47] "TCGA.VQ.A91A.01A.11R.A414.31" "TCGA.F1.A72C.01A.21R.A33Y.31"
##  [49] "TCGA.D7.8578.01A.21R.2343.13" "TCGA.CG.5732.01A.11R.1602.13"
##  [51] "TCGA.BR.6707.01A.11R.1884.13" "TCGA.VQ.AA6I.01A.11R.A414.31"
##  [53] "TCGA.BR.8060.01A.11R.2343.13" "TCGA.F1.A448.01A.11R.A24K.31"
##  [55] "TCGA.VQ.A8E7.01B.11R.A414.31" "TCGA.RD.A8N9.01A.12R.A39E.31"
##  [57] "TCGA.HU.A4GF.01A.11R.A24K.31" "TCGA.BR.4367.01A.01R.1157.13"
##  [59] "TCGA.VQ.A923.01A.11R.A414.31" "TCGA.CG.5720.01A.11R.1602.13"
##  [61] "TCGA.HU.8602.01A.11R.2402.13" "TCGA.CG.4477.01A.01R.1157.13"
##  [63] "TCGA.D7.6822.01A.11R.1884.13" "TCGA.CD.8526.01A.11R.2343.13"
##  [65] "TCGA.D7.A6EY.01A.21R.A31P.31" "TCGA.CD.5798.01A.11R.1602.13"
##  [67] "TCGA.R5.A805.01A.11R.A36D.31" "TCGA.BR.6455.01A.11R.1802.13"
##  [69] "TCGA.HU.A4GJ.01A.11R.A251.31" "TCGA.BR.8297.01A.12R.2343.13"
##  [71] "TCGA.BR.8372.01A.11R.2343.13" "TCGA.HU.A4GY.01A.21R.A24K.31"
##  [73] "TCGA.VQ.A94P.01A.13R.A414.31" "TCGA.BR.8590.01A.11R.2402.13"
##  [75] "TCGA.BR.7703.01A.11R.2055.13" "TCGA.VQ.A91Y.01A.11R.A414.31"
##  [77] "TCGA.HU.A4H6.01A.11R.A251.31" "TCGA.VQ.A8PC.01A.11R.A39E.31"
##  [79] "TCGA.R5.A7ZF.01A.11R.A354.31" "TCGA.HU.A4GN.01A.11R.A251.31"
##  [81] "TCGA.BR.8286.01A.12R.2343.13" "TCGA.D7.6818.01A.11R.1884.13"
##  [83] "TCGA.CG.4442.01A.01R.1157.13" "TCGA.VQ.A91S.01A.11R.A414.31"
##  [85] "TCGA.MX.A5UG.01A.21R.A31P.31" "TCGA.D7.A748.01A.12R.A32D.31"
##  [87] "TCGA.VQ.AA6K.01A.11R.A414.31" "TCGA.BR.8371.01A.11R.2343.13"
##  [89] "TCGA.VQ.AA6D.01A.11R.A414.31" "TCGA.CG.4469.01A.01R.1157.13"
##  [91] "TCGA.CG.4472.01A.01R.1157.13" "TCGA.MX.A5UJ.01A.11R.A31P.31"
##  [93] "TCGA.VQ.A91U.01A.11R.A414.31" "TCGA.VQ.A91E.01A.31R.A414.31"
##  [95] "TCGA.HU.A4GP.01A.11R.A251.31" "TCGA.BR.8682.01A.11R.2402.13"
##  [97] "TCGA.BR.8361.01A.11R.2343.13" "TCGA.VQ.AA6A.01A.11R.A414.31"
##  [99] "TCGA.R5.A7O7.01A.11R.A33Y.31" "TCGA.CG.4444.01A.01R.1157.13"
## [101] "TCGA.BR.A4J4.01A.12R.A251.31" "TCGA.BR.8485.01A.11R.2402.13"
## [103] "TCGA.BR.A4CR.01A.11R.A24K.31" "TCGA.BR.8487.01A.11R.2402.13"
## [105] "TCGA.D7.A4Z0.01A.22R.A251.31" "TCGA.FP.8099.01A.11R.2343.13"
## [107] "TCGA.BR.A44T.01A.32R.A24K.31" "TCGA.BR.8680.01A.11R.2402.13"
## [109] "TCGA.HU.8243.01A.11R.2343.13" "TCGA.D7.A6F2.01A.12R.A31P.31"
## [111] "TCGA.CG.4474.01A.02R.1157.13" "TCGA.VQ.A91X.01A.12R.A414.31"
## [113] "TCGA.BR.8677.01A.11R.2402.13" "TCGA.RD.A8N0.01A.12R.A36D.31"
## [115] "TCGA.IN.AB1X.01A.11R.A39E.31" "TCGA.RD.A8N1.01A.12R.A36D.31"
## [117] "TCGA.EQ.8122.01A.11R.2343.13" "TCGA.B7.A5TI.01A.11R.A31P.31"
## [119] "TCGA.HU.A4H4.01A.21R.A251.31" "TCGA.IN.AB1V.01A.21R.A414.31"
## [121] "TCGA.BR.7722.01A.31R.2203.13" "TCGA.HF.7134.01A.11R.2055.13"
## [123] "TCGA.BR.7715.01A.11R.2055.13" "TCGA.CG.5722.01A.21R.1602.13"
## [125] "TCGA.BR.8369.01A.11R.2343.13" "TCGA.F1.6875.01A.11R.2055.13"
## [127] "TCGA.RD.A8N2.01A.12R.A36D.31" "TCGA.BR.A453.01A.11R.A24K.31"
## [129] "TCGA.BR.6454.01A.11R.1802.13" "TCGA.HU.A4H5.01A.21R.A251.31"
## [131] "TCGA.VQ.A91V.01A.11R.A414.31" "TCGA.BR.A4IU.01A.22R.A251.31"
## [133] "TCGA.BR.7851.01A.11R.2203.13" "TCGA.BR.8367.01A.11R.2343.13"
## [135] "TCGA.HU.A4G9.01A.11R.A24K.31" "TCGA.KB.A6F7.01A.12R.A32D.31"
## [137] "TCGA.CD.A48A.01A.12R.A36D.31" "TCGA.BR.8678.01A.11R.2402.13"
## [139] "TCGA.VQ.A94U.01A.12R.A414.31" "TCGA.VQ.A927.01A.12R.A414.31"
## [141] "TCGA.BR.A4PD.01A.11R.A251.31" "TCGA.BR.7958.01A.21R.2343.13"
## [143] "TCGA.D7.6521.01A.11R.1802.13" "TCGA.VQ.A924.01A.11R.A414.31"
## [145] "TCGA.IN.A6RO.01A.12R.A33Y.31" "TCGA.RD.A7BT.01A.11R.A33Y.31"
## [147] "TCGA.BR.4191.01A.02R.1131.13" "TCGA.D7.A6EZ.01A.11R.A31P.31"
## [149] "TCGA.CG.5723.01A.11R.1602.13" "TCGA.CG.5726.01A.11R.1602.13"
## [151] "TCGA.CG.4440.01A.01R.1157.13" "TCGA.VQ.AA68.01A.11R.A414.31"
## [153] "TCGA.VQ.A92D.01A.11R.A414.31" "TCGA.CG.5734.01A.11R.1602.13"
## [155] "TCGA.BR.A4PE.01A.31R.A251.31" "TCGA.IN.8462.01A.11R.2343.13"
## [157] "TCGA.HU.A4G3.01A.11R.A24K.31" "TCGA.HF.7132.01A.11R.2055.13"
## [159] "TCGA.FP.8210.01A.11R.2343.13" "TCGA.D7.5578.01A.01R.1602.13"
## [161] "TCGA.BR.6564.01A.12R.1884.13" "TCGA.BR.8365.01A.21R.2343.13"
## [163] "TCGA.BR.8078.01A.11R.2343.13" "TCGA.CG.4304.01A.01R.1157.13"
## [165] "TCGA.B7.A5TJ.01A.11R.A31P.31" "TCGA.D7.A6EX.01A.11R.A31P.31"
## [167] "TCGA.D7.8570.01A.11R.2343.13" "TCGA.CD.5800.01A.11R.1602.13"
## [169] "TCGA.HU.A4H3.01A.21R.A251.31" "TCGA.BR.4371.01A.01R.1157.13"
## [171] "TCGA.HF.7131.01A.11R.2055.13" "TCGA.D7.6518.01A.11R.1802.13"
## [173] "TCGA.BR.8368.01A.11R.2343.13" "TCGA.RD.A8NB.01A.12R.A39E.31"
## [175] "TCGA.HU.A4G8.01A.11R.A251.31" "TCGA.IP.7968.01A.11R.2203.13"
## [177] "TCGA.IN.A6RI.01A.11R.A32D.31" "TCGA.VQ.A8P5.01A.11R.A39E.31"
## [179] "TCGA.BR.4201.01A.01R.1131.13" "TCGA.BR.4362.01A.01R.1157.13"
## [181] "TCGA.CG.5725.01A.11R.1602.13" "TCGA.BR.7957.01A.11R.2203.13"
## [183] "TCGA.BR.4280.01A.01R.1131.13" "TCGA.FP.A8CX.01A.11R.A36D.31"
## [185] "TCGA.BR.8591.01A.11R.2402.13" "TCGA.D7.8575.01A.11R.2343.13"
## [187] "TCGA.CD.8534.01A.11R.2343.13" "TCGA.BR.8362.01A.11R.2343.13"
## [189] "TCGA.HF.A5NB.01A.11R.A31P.31" "TCGA.D7.A4YT.01A.11R.A251.31"
## [191] "TCGA.BR.4256.01A.01R.1131.13" "TCGA.BR.4255.01A.01R.1131.13"
## [193] "TCGA.BR.8289.01A.11R.2343.13" "TCGA.BR.8366.01A.11R.2343.13"
## [195] "TCGA.VQ.A94O.01A.11R.A414.31" "TCGA.D7.A4YU.01A.21R.A251.31"
## [197] "TCGA.BR.6565.01A.11R.1802.13" "TCGA.CG.4466.01A.01R.1157.13"
## [199] "TCGA.VQ.A8PQ.01A.11R.A414.31" "TCGA.BR.8080.01A.11R.2343.13"
## [201] "TCGA.KB.A93J.01A.11R.A39E.31" "TCGA.CG.4441.01A.01R.1802.13"
## [203] "TCGA.VQ.A8DZ.01A.11R.A36D.31" "TCGA.VQ.A8PM.01A.21R.A414.31"
## [205] "TCGA.VQ.A8PP.01A.21R.A414.31" "TCGA.D7.A74A.01A.11R.A32D.31"
## [207] "TCGA.D7.A6EV.01A.11R.A31P.31" "TCGA.HU.A4GX.01A.12R.A251.31"
## [209] "TCGA.3M.AB47.01A.22R.A414.31" "TCGA.VQ.A922.01A.11R.A414.31"
## [211] "TCGA.BR.4279.01A.01R.1131.13" "TCGA.RD.A8MV.01A.11R.A36D.31"
## [213] "TCGA.VQ.A91Z.01A.11R.A414.31" "TCGA.CG.4437.01A.01R.1802.13"
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## [219] "TCGA.VQ.A8PJ.01A.11R.A414.31" "TCGA.BR.4267.01A.01R.1131.13"
## [221] "TCGA.CG.4476.01A.01R.1157.13" "TCGA.BR.6566.01A.11R.1802.13"
## [223] "TCGA.BR.A4J2.01A.21R.A251.31" "TCGA.CG.5721.01A.11R.1602.13"
## [225] "TCGA.EQ.A4SO.01A.11R.A251.31" "TCGA.FP.A4BE.01A.12R.A24K.31"
## [227] "TCGA.F1.6874.01A.11R.1884.13" "TCGA.VQ.AA6G.01A.11R.A414.31"
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## [233] "TCGA.BR.A4J8.01A.11R.A251.31" "TCGA.BR.4366.01A.01R.1157.13"
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## [239] "TCGA.VQ.A8PK.01A.12R.A414.31" "TCGA.CD.8531.01A.11R.2343.13"
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## [249] "TCGA.CD.5801.01A.11R.1602.13" "TCGA.CD.8530.01A.11R.2343.13"
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## [253] "TCGA.BR.8381.01A.11R.2402.13" "TCGA.VQ.A8P2.01A.11R.A36D.31"
## [255] "TCGA.HU.8249.01A.11R.A36D.31" "TCGA.VQ.A8DT.01A.11R.A36D.31"
## [257] "TCGA.BR.8380.01A.11R.2343.13" "TCGA.CG.4305.01A.01R.1157.13"
## [259] "TCGA.BR.8588.01A.11R.2402.13" "TCGA.D7.6526.01A.11R.1802.13"
## [261] "TCGA.BR.8592.01A.11R.2402.13" "TCGA.BR.6801.01A.11R.1884.13"
## [263] "TCGA.CG.4301.01A.01R.1157.13" "TCGA.BR.7707.01A.11R.2055.13"
## [265] "TCGA.CD.8535.01A.11R.2343.13" "TCGA.CG.4443.01A.01R.1157.13"
## [267] "TCGA.IN.A6RL.01A.11R.A32D.31" "TCGA.VQ.AA6J.01A.11R.A414.31"
## [269] "TCGA.RD.A8MW.01A.11R.A36D.31" "TCGA.VQ.A91Q.01A.12R.A414.31"
## [271] "TCGA.HU.A4H0.01A.11R.A251.31" "TCGA.CD.8524.01A.11R.2343.13"
## [273] "TCGA.BR.4370.01A.01R.1157.13" "TCGA.BR.7717.01A.11R.2055.13"
## [275] "TCGA.CG.4462.01A.01R.1157.13" "TCGA.HF.7136.01A.11R.2055.13"
## [277] "TCGA.BR.8686.01A.11R.2402.13" "TCGA.D7.8579.01A.11R.2343.13"
## [279] "TCGA.BR.8484.01A.11R.2402.13" "TCGA.BR.8363.01A.11R.2343.13"
## [281] "TCGA.HF.7133.01A.11R.2055.13" "TCGA.B7.5816.01A.21R.1602.13"
## [283] "TCGA.D7.8573.01A.11R.2343.13" "TCGA.D7.6527.01A.11R.1802.13"
## [285] "TCGA.BR.4253.01A.01R.1131.13" "TCGA.RD.A7BW.01A.11R.A32D.31"
## [287] "TCGA.CG.4465.01A.01R.1157.13" "TCGA.CD.8532.01A.11R.2343.13"
## [289] "TCGA.FP.7735.01A.11R.2055.13" "TCGA.BR.7197.01A.11R.2203.13"
## [291] "TCGA.BR.8679.01A.11R.2402.13" "TCGA.VQ.AA69.01A.11R.A414.31"
## [293] "TCGA.D7.A4YX.01A.11R.A251.31" "TCGA.FP.A9TM.01A.11R.A39E.31"
## [295] "TCGA.HU.8244.01A.11R.2343.13" "TCGA.BR.8296.01A.11R.2343.13"
## [297] "TCGA.D7.6525.01A.11R.1802.13" "TCGA.CD.A4MJ.01A.11R.A251.31"
## [299] "TCGA.VQ.A94T.01A.11R.A414.31" "TCGA.BR.A4IY.01A.11R.A251.31"
## [301] "TCGA.CG.5717.01A.11R.1602.13" "TCGA.ZA.A8F6.01A.23R.A36D.31"
## [303] "TCGA.B7.A5TN.01A.21R.A31P.31" "TCGA.BR.8589.01A.11R.2402.13"
## [305] "TCGA.BR.8373.01A.11R.2343.13" "TCGA.BR.8683.01A.11R.2402.13"
## [307] "TCGA.IN.7808.01A.11R.2203.13" "TCGA.VQ.A91W.01A.11R.A414.31"
## [309] "TCGA.FP.8209.01A.11R.2343.13" "TCGA.VQ.A8PF.01A.11R.A414.31"
## [311] "TCGA.VQ.A8PX.01A.12R.A414.31" "TCGA.VQ.A91D.01A.11R.A414.31"
## [313] "TCGA.HU.A4GC.01A.12R.A251.31" "TCGA.D7.6519.01A.11R.1802.13"
## [315] "TCGA.IN.7806.01A.11R.2055.13" "TCGA.HU.A4GT.01A.21R.A251.31"
## [317] "TCGA.HU.A4H8.01A.11R.A251.31" "TCGA.CD.5813.01A.11R.1602.13"
## [319] "TCGA.BR.A4J9.01A.12R.A251.31" "TCGA.R5.A7ZE.01B.11R.A354.31"
## [321] "TCGA.CG.4460.01A.01R.1157.13" "TCGA.D7.6528.01A.11R.1802.13"
## [323] "TCGA.VQ.A8PU.01A.12R.A414.31" "TCGA.CG.4436.01A.01R.1157.13"
## [325] "TCGA.BR.6458.01A.11R.1802.13" "TCGA.VQ.A8PO.01A.11R.A414.31"
## [327] "TCGA.BR.8382.01A.11R.2402.13" "TCGA.D7.A4YV.01A.11R.A251.31"
## [329] "TCGA.CG.5719.01A.11R.1602.13" "TCGA.CD.5804.01A.12R.2055.13"
## [331] "TCGA.D7.6522.01A.11R.1802.13" "TCGA.CD.8528.01A.11R.2343.13"
## [333] "TCGA.D7.8572.01A.11R.2343.13" "TCGA.D7.6815.01A.11R.1884.13"
## [335] "TCGA.BR.4357.01A.01R.1157.13" "TCGA.BR.6453.01A.11R.1802.13"
## [337] "TCGA.VQ.A928.01A.11R.A414.31" "TCGA.D7.6520.01A.11R.1802.13"
## [339] "TCGA.CD.8533.01A.11R.2343.13" "TCGA.B7.5818.01A.11R.1602.13"
## [341] "TCGA.FP.A4BF.01A.12R.A36D.31" "TCGA.D7.6524.01A.11R.1802.13"
## [343] "TCGA.VQ.A94R.01A.11R.A414.31" "TCGA.FP.7916.01A.11R.2203.13"
## [345] "TCGA.BR.4294.01A.01R.1131.13" "TCGA.BR.4368.01A.01R.1157.13"
## [347] "TCGA.D7.6817.01A.11R.1884.13" "TCGA.BR.8384.01A.21R.2402.13"
## [349] "TCGA.BR.7723.01A.11R.2055.13" "TCGA.HJ.7597.01A.21R.2203.13"
## [351] "TCGA.KB.A93G.01A.11R.A39E.31" "TCGA.IN.8663.01A.11R.2402.13"
## [353] "TCGA.D7.A747.01A.22R.A33Y.31" "TCGA.CG.4449.01A.01R.1157.13"
## [355] "TCGA.BR.8081.01A.11R.2343.13" "TCGA.VQ.AA64.01A.11R.A414.31"
## [357] "TCGA.D7.8574.01A.13R.2343.13" "TCGA.MX.A663.01A.11R.A31P.31"
## [359] "TCGA.VQ.A91N.01A.11R.A414.31" "TCGA.HU.8238.01A.11R.2343.13"
## [361] "TCGA.BR.8483.01A.31R.2402.13" "TCGA.CG.4306.01A.01R.1157.13"
## [363] "TCGA.BR.8291.01A.11R.2343.13" "TCGA.HU.8604.01A.11R.2402.13"
## [365] "TCGA.VQ.A8P8.01A.11R.A39E.31" "TCGA.CG.4475.01A.01R.1157.13"
## [367] "TCGA.VQ.A91K.01A.11R.A414.31" "TCGA.BR.8687.01A.11R.2402.13"
## [369] "TCGA.CD.A486.01A.11R.A24K.31" "TCGA.BR.8364.01A.11R.2343.13"
## [371] "TCGA.FP.8211.01A.11R.2343.13" "TCGA.BR.8058.01A.31R.2343.13"
## [373] "TCGA.CD.8529.01A.11R.2343.13" "TCGA.BR.4363.01A.01R.1157.13"
## [375] "TCGA.D7.A6F0.01A.11R.A31P.31" "TCGA.BR.8077.01A.11R.2343.13"
## [377] "TCGA.HU.A4GU.01A.11R.A251.31" "TCGA.BR.7901.01A.11R.2203.13"
## [379] "TCGA.D7.6820.01A.11R.1884.13" "TCGA.RD.A8N6.01A.11R.A36D.31"
## [381] "TCGA.BR.8486.01A.31R.2402.13" "TCGA.CD.8536.01A.11R.2343.13"
df.t.tcga.FAM86A<-df.t.tcga %>% 
  filter(Hugo_Symbol == 'FAM86A')

head(df.t.tcga.FAM86A)[2]
##   Entrez_Gene_Id
## 1         196483
dim(df.t.tcga.FAM86A)
## [1]   1 382
#transposing
df.t.tcga.FAM86A<-df.t.tcga.FAM86A %>% 
  gather(Patients,FPKM,3:ncol(.))

dim(df.t.tcga.FAM86A)
## [1] 380   4
head(df.t.tcga.FAM86A)
##   Hugo_Symbol Entrez_Gene_Id                     Patients   FPKM
## 1      FAM86A         196483 TCGA.BR.6457.01A.21R.1802.13 325.29
## 2      FAM86A         196483 TCGA.VQ.A8PD.01A.11R.A414.31 215.77
## 3      FAM86A         196483 TCGA.BR.6803.01A.11R.1884.13 346.29
## 4      FAM86A         196483 TCGA.VQ.A8E3.01A.11R.A39E.31 277.20
## 5      FAM86A         196483 TCGA.CG.5718.01A.11R.1602.13 351.14
## 6      FAM86A         196483 TCGA.VQ.A8E2.01A.11R.A36D.31 356.05
df.t.tcga.FAM86A.log2<-df.t.tcga.FAM86A %>% 
  mutate(log2FPKM=log(FPKM,base = 2))
head(df.t.tcga.FAM86A.log2)
##   Hugo_Symbol Entrez_Gene_Id                     Patients   FPKM log2FPKM
## 1      FAM86A         196483 TCGA.BR.6457.01A.21R.1802.13 325.29 8.345583
## 2      FAM86A         196483 TCGA.VQ.A8PD.01A.11R.A414.31 215.77 7.753350
## 3      FAM86A         196483 TCGA.BR.6803.01A.11R.1884.13 346.29 8.435837
## 4      FAM86A         196483 TCGA.VQ.A8E3.01A.11R.A39E.31 277.20 8.114783
## 5      FAM86A         196483 TCGA.CG.5718.01A.11R.1602.13 351.14 8.455903
## 6      FAM86A         196483 TCGA.VQ.A8E2.01A.11R.A36D.31 356.05 8.475936
###############combine the 3 data to 1###########
s.gtex<-df.gtex.FAM86A.log2 %>% 
  mutate(data='GTEx') %>% 
  dplyr::select('data','log2FPKM')
head(s.gtex)
##   data log2FPKM
## 1 GTEx 7.813589
## 2 GTEx 7.783457
## 3 GTEx 6.928252
## 4 GTEx 7.532239
## 5 GTEx 7.421644
## 6 GTEx 7.532239
dim(s.gtex)
## [1] 192   2
s.nor<-df.n.tcga.FAM86A.log2 %>% 
  mutate(data='NAT') %>% 
  dplyr::select('data','log2FPKM')

s.tumor<-df.t.tcga.FAM86A.log2 %>% 
  mutate(data='Tumor') %>% 
  dplyr::select('data','log2FPKM')

#binding rows
unify.FAM86A<-rbind(s.gtex,s.nor,s.tumor)

head(unify.FAM86A)
##   data log2FPKM
## 1 GTEx 7.813589
## 2 GTEx 7.783457
## 3 GTEx 6.928252
## 4 GTEx 7.532239
## 5 GTEx 7.421644
## 6 GTEx 7.532239
dim(unify.FAM86A)
## [1] 605   2
View(unify.FAM86A)
count(unify.FAM86A,data)
##    data   n
## 1  GTEx 192
## 2   NAT  33
## 3 Tumor 380

## 
##  Kruskal-Wallis rank sum test
## 
## data:  log2FPKM by source
## Kruskal-Wallis chi-squared = 55.539, df = 2, p-value = 8.706e-13
## 
##  Pairwise comparisons using Wilcoxon rank sum test with continuity correction 
## 
## data:  a$log2FPKM and a$source 
## 
##             GTEx    Normal TCGA
## Normal TCGA 0.63    -          
## Tumor TCGA  2.1e-11 8.9e-05    
## 
## P value adjustment method: BH

TCGA analysis for subtype expression

####IMPORTANT! Please download the github version to use the most recent version of TCGAbiolinks
devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks",force = TRUE)
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## 
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##  C:\Users\nuraz\AppData\Local\Temp\RtmpYDVDl6\downloaded_packages
## * checking for file 'C:\Users\nuraz\AppData\Local\Temp\RtmpYDVDl6\remotes34bc49f643d7\BioinformaticsFMRP-TCGAbiolinks-3140986/DESCRIPTION' ... OK
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## * checking for LF line-endings in source and make files and shell scripts
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## * building 'TCGAbiolinks_2.25.0.tar.gz'
## 
devtools::install_github(repo = "ELELAB/TCGAbiolinks")
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## Biostrings   (2.60.2   -> 2.62.0  ) [CRAN]
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## RSQLite      (2.2.8    -> 2.2.14  ) [CRAN]
## IRanges      (2.26.0   -> 2.28.0  ) [CRAN]
## XML          (3.99-0.8 -> 3.99-0.9) [CRAN]
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## * preparing 'TCGAbiolinks':
## * checking DESCRIPTION meta-information ... OK
## * checking for LF line-endings in source and make files and shell scripts
## * checking for empty or unneeded directories
## * building 'TCGAbiolinks_2.7.9.tar.gz'
## 
library(TCGAbiolinks)
library(SummarizedExperiment)
library(recount)
###conversion of uuids to TCGA barcodes
library(TCGAutils)
library(limma)
library(biomaRt)

query <- GDCquery(project = "TCGA-STAD",
                  data.category = "Gene expression",
                  data.type = "Gene expression quantification",
                  platform = "Illumina HiSeq",
                  file.type = "results",
                  legacy = TRUE,
                  sample.type = c("Primary Tumor"))

GDCdownload(query)
stad.exp<-GDCprepare(query,
                     save = TRUE,
                     summarizedExperiment = TRUE,
                     save.filename = "STADIllumina_HiSeq.rda")
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head(stad.exp)
## class: RangedSummarizedExperiment 
## dim: 6 415 
## metadata(1): data_release
## assays(2): raw_count scaled_estimate
## rownames(6): A1BG|1 A2M|2 ... SERPINA3|12 AADAC|13
## rowData names(4): gene_id entrezgene ensembl_gene_id
##   transcript_id.transcript_id_TCGA-CD-8536-01A-11R-2343-13
## colnames(415): TCGA-CD-8536-01A-11R-2343-13
##   TCGA-BR-8077-01A-11R-2343-13 ... TCGA-VQ-A8PQ-01A-11R-A414-31
##   TCGA-CD-8535-01A-11R-2343-13
## colData names(109): barcode patient ... paper_CIMP.Category
##   paper_stringAsFactor
rse <- get(load("STADIllumina_HiSeq.rda"))


dataClin_STAD <- GDCquery_clinic("TCGA-STAD", "Clinical")
write.csv(dataClin_STAD, "dataClin_STAD.csv")

dataPrep_STAD<-TCGAanalyze_Preprocessing(rse,
                                         cor.cut = .5,
                                         datatype = "raw_count",
                                         filename = "STAD_IlluminaHiSeq_RNASeqV2.png")
# normalization of genes
dataNorm<-TCGAanalyze_Normalization(tabDF = dataPrep_STAD,geneInfo = geneInfo,method = "gcContent")

head(dataNorm)
##           TCGA-3M-AB46-01A-11R-A414-31 TCGA-3M-AB47-01A-22R-A414-31
## 100133144                           37                           36
## 100134869                           50                           18
## 155060                             555                          387
## 280660                               0                            0
## 8225                               990                         1502
## 90288                               33                            6
##           TCGA-B7-5816-01A-21R-1602-13 TCGA-B7-5818-01A-11R-1602-13
## 100133144                           16                           38
## 100134869                           54                          247
## 155060                             105                          333
## 280660                               0                            0
## 8225                               996                         1314
## 90288                                5                           32
##           TCGA-B7-A5TI-01A-11R-A31P-31 TCGA-B7-A5TJ-01A-11R-A31P-31
## 100133144                           39                          106
## 100134869                           53                           87
## 155060                             179                          880
## 280660                               0                            0
## 8225                              1584                         2202
## 90288                                4                            0
##           TCGA-B7-A5TK-01A-12R-A36D-31 TCGA-B7-A5TN-01A-21R-A31P-31
## 100133144                           19                           57
## 100134869                            0                           56
## 155060                             134                          147
## 280660                               0                            0
## 8225                               875                          708
## 90288                               21                            7
##           TCGA-BR-4187-01A-01R-1131-13 TCGA-BR-4191-01A-02R-1131-13
## 100133144                            6                           36
## 100134869                            2                           28
## 155060                              70                          455
## 280660                               0                            0
## 8225                               914                          742
## 90288                                0                            2
##           TCGA-BR-4201-01A-01R-1131-13 TCGA-BR-4253-01A-01R-1131-13
## 100133144                           31                           27
## 100134869                           11                           35
## 155060                             358                          499
## 280660                               0                            0
## 8225                               688                         1217
## 90288                               10                           23
##           TCGA-BR-4255-01A-01R-1131-13 TCGA-BR-4256-01A-01R-1131-13
## 100133144                            0                            5
## 100134869                           15                           21
## 155060                              68                          153
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## 8225                               859                         1246
## 90288                               11                           16
##           TCGA-IN-7806-01A-11R-2055-13 TCGA-IN-7808-01A-11R-2203-13
## 100133144                          150                          104
## 100134869                           86                          107
## 155060                             719                          750
## 280660                               0                            0
## 8225                              1178                         1123
## 90288                                4                            3
##           TCGA-IN-8462-01A-11R-2343-13 TCGA-IN-8663-01A-11R-2402-13
## 100133144                           96                          214
## 100134869                           56                          122
## 155060                             157                          380
## 280660                               0                            0
## 8225                               723                          312
## 90288                               10                            3
##           TCGA-IN-A6RI-01A-11R-A32D-31 TCGA-IN-A6RJ-01A-21R-A33Y-31
## 100133144                           33                          351
## 100134869                           62                          381
## 155060                             117                          387
## 280660                             106                            0
## 8225                              1918                         1305
## 90288                               49                            0
##           TCGA-IN-A6RL-01A-11R-A32D-31 TCGA-IN-A6RN-01A-12R-A33Y-31
## 100133144                           81                           99
## 100134869                           63                          136
## 155060                             138                          298
## 280660                               0                            0
## 8225                              1161                         1401
## 90288                                1                           12
##           TCGA-IN-A6RO-01A-12R-A33Y-31 TCGA-IN-A6RR-01A-12R-A32D-31
## 100133144                          131                           29
## 100134869                          128                           60
## 155060                             350                          188
## 280660                               0                            0
## 8225                               953                         1799
## 90288                               12                            2
##           TCGA-IN-A6RS-01A-12R-A354-31 TCGA-IN-A7NR-01A-11R-A354-31
## 100133144                           63                          143
## 100134869                           27                          196
## 155060                             208                          156
## 280660                               0                            0
## 8225                               729                          989
## 90288                                5                            0
##           TCGA-IN-A7NT-01A-21R-A354-31 TCGA-IN-A7NU-01A-22R-A354-31
## 100133144                           45                           16
## 100134869                           85                           33
## 155060                             286                          153
## 280660                               0                            0
## 8225                              1151                          826
## 90288                               35                           13
##           TCGA-IN-AB1V-01A-21R-A414-31 TCGA-IN-AB1X-01A-11R-A39E-31
## 100133144                          263                          135
## 100134869                          273                           67
## 155060                             446                          365
## 280660                               0                            0
## 8225                              1385                          971
## 90288                               23                           29
##           TCGA-IP-7968-01A-11R-2203-13 TCGA-KB-A6F7-01A-12R-A32D-31
## 100133144                           26                           54
## 100134869                           30                           36
## 155060                             468                          219
## 280660                               0                           20
## 8225                               680                         1184
## 90288                               60                           16
##           TCGA-KB-A93G-01A-11R-A39E-31 TCGA-KB-A93H-01A-11R-A39E-31
## 100133144                           77                          159
## 100134869                           22                          118
## 155060                             474                          341
## 280660                               0                            0
## 8225                              1023                         2856
## 90288                                2                           18
##           TCGA-KB-A93J-01A-11R-A39E-31 TCGA-MX-A5UG-01A-21R-A31P-31
## 100133144                           60                           30
## 100134869                           57                           11
## 155060                             338                          482
## 280660                               0                            0
## 8225                              1647                         1190
## 90288                               11                           11
##           TCGA-MX-A5UJ-01A-11R-A31P-31 TCGA-MX-A663-01A-11R-A31P-31
## 100133144                           87                            6
## 100134869                           47                            6
## 155060                             329                          240
## 280660                               0                            0
## 8225                              1045                          764
## 90288                                6                           11
##           TCGA-MX-A666-01A-11R-A31P-31 TCGA-R5-A7O7-01A-11R-A33Y-31
## 100133144                           23                           55
## 100134869                           16                           83
## 155060                             554                          266
## 280660                               0                            0
## 8225                              1031                         1852
## 90288                                8                           85
##           TCGA-R5-A7ZE-01B-11R-A354-31 TCGA-R5-A7ZF-01A-11R-A354-31
## 100133144                           81                           53
## 100134869                           57                           45
## 155060                             164                          295
## 280660                               0                            2
## 8225                              1466                         1376
## 90288                               10                           17
##           TCGA-R5-A7ZI-01A-11R-A354-31 TCGA-R5-A7ZR-01A-11R-A354-31
## 100133144                           84                           30
## 100134869                           93                           30
## 155060                             389                          137
## 280660                               0                            0
## 8225                              2202                         2510
## 90288                               19                            6
##           TCGA-R5-A805-01A-11R-A36D-31 TCGA-RD-A7BS-01A-11R-A32D-31
## 100133144                           98                           67
## 100134869                          138                           31
## 155060                             228                          140
## 280660                               0                            0
## 8225                               722                          655
## 90288                               19                            4
##           TCGA-RD-A7BT-01A-11R-A33Y-31 TCGA-RD-A7BW-01A-11R-A32D-31
## 100133144                          116                           13
## 100134869                          108                           21
## 155060                             402                          284
## 280660                               0                            0
## 8225                              1202                          795
## 90288                                6                            0
##           TCGA-RD-A7C1-01A-11R-A32D-31 TCGA-RD-A8MV-01A-11R-A36D-31
## 100133144                            0                           53
## 100134869                           18                           91
## 155060                             326                          476
## 280660                               0                            0
## 8225                               628                          831
## 90288                                0                            8
##           TCGA-RD-A8MW-01A-11R-A36D-31 TCGA-RD-A8N0-01A-12R-A36D-31
## 100133144                           17                          102
## 100134869                           20                           47
## 155060                             126                          382
## 280660                               0                            0
## 8225                              1605                         1416
## 90288                               11                            8
##           TCGA-RD-A8N1-01A-12R-A36D-31 TCGA-RD-A8N2-01A-12R-A36D-31
## 100133144                           53                           29
## 100134869                           25                           16
## 155060                             551                          726
## 280660                               0                            0
## 8225                              1837                         1342
## 90288                                9                           12
##           TCGA-RD-A8N4-01A-21R-A36D-31 TCGA-RD-A8N5-01A-12R-A36D-31
## 100133144                           69                           69
## 100134869                           20                           23
## 155060                             408                          475
## 280660                               0                            0
## 8225                               727                          835
## 90288                               48                           31
##           TCGA-RD-A8N6-01A-11R-A36D-31 TCGA-RD-A8N9-01A-12R-A39E-31
## 100133144                           53                           39
## 100134869                           23                           23
## 155060                             203                          349
## 280660                               0                            2
## 8225                               652                         1327
## 90288                               12                           16
##           TCGA-RD-A8NB-01A-12R-A39E-31 TCGA-SW-A7EA-01A-12R-A354-31
## 100133144                           57                           78
## 100134869                           26                           51
## 155060                             344                          252
## 280660                               0                            0
## 8225                              1308                         1200
## 90288                                9                           13
##           TCGA-SW-A7EB-01A-11R-A354-31 TCGA-VQ-A8DT-01A-11R-A36D-31
## 100133144                           25                           63
## 100134869                           24                           31
## 155060                             116                          368
## 280660                               0                            0
## 8225                              1108                         2047
## 90288                               14                           72
##           TCGA-VQ-A8DU-01A-11R-A36D-31 TCGA-VQ-A8DV-01A-12R-A36D-31
## 100133144                           19                           11
## 100134869                           61                           10
## 155060                             274                          428
## 280660                               0                            0
## 8225                              1224                         1760
## 90288                               29                           22
##           TCGA-VQ-A8DZ-01A-11R-A36D-31 TCGA-VQ-A8E0-01A-11R-A414-31
## 100133144                           39                           51
## 100134869                           64                           19
## 155060                             165                          158
## 280660                               0                            0
## 8225                               923                         2299
## 90288                                4                           56
##           TCGA-VQ-A8E2-01A-11R-A36D-31 TCGA-VQ-A8E3-01A-11R-A39E-31
## 100133144                           44                           56
## 100134869                           51                           32
## 155060                             425                          430
## 280660                               0                            0
## 8225                              1371                          845
## 90288                               51                           11
##           TCGA-VQ-A8E7-01B-11R-A414-31 TCGA-VQ-A8P2-01A-11R-A36D-31
## 100133144                           93                          118
## 100134869                           45                          102
## 155060                             312                          432
## 280660                               0                            0
## 8225                              1624                         1809
## 90288                               17                           16
##           TCGA-VQ-A8P3-01A-11R-A36D-31 TCGA-VQ-A8P5-01A-11R-A39E-31
## 100133144                           35                           97
## 100134869                           78                           40
## 155060                             300                          283
## 280660                               7                            0
## 8225                               841                         1770
## 90288                               92                           10
##           TCGA-VQ-A8P8-01A-11R-A39E-31 TCGA-VQ-A8PB-01A-11R-A39E-31
## 100133144                           24                          116
## 100134869                           22                           72
## 155060                             222                          408
## 280660                               0                            0
## 8225                              1172                         1829
## 90288                               23                           17
##           TCGA-VQ-A8PC-01A-11R-A39E-31 TCGA-VQ-A8PD-01A-11R-A414-31
## 100133144                          100                           50
## 100134869                           33                           28
## 155060                             318                          632
## 280660                               0                            0
## 8225                               683                         1418
## 90288                               14                           10
##           TCGA-VQ-A8PE-01A-11R-A414-31 TCGA-VQ-A8PF-01A-11R-A414-31
## 100133144                           39                           54
## 100134869                           15                           35
## 155060                             318                          425
## 280660                               0                            0
## 8225                              2582                         1683
## 90288                                4                            9
##           TCGA-VQ-A8PH-01A-12R-A414-31 TCGA-VQ-A8PJ-01A-11R-A414-31
## 100133144                          124                           74
## 100134869                           44                           32
## 155060                             435                          146
## 280660                               0                            0
## 8225                               622                         1394
## 90288                               11                           30
##           TCGA-VQ-A8PK-01A-12R-A414-31 TCGA-VQ-A8PM-01A-21R-A414-31
## 100133144                           56                           54
## 100134869                           22                           23
## 155060                             186                          272
## 280660                               0                            0
## 8225                              1648                         3070
## 90288                               28                           13
##           TCGA-VQ-A8PO-01A-11R-A414-31 TCGA-VQ-A8PP-01A-21R-A414-31
## 100133144                           72                          152
## 100134869                           34                           76
## 155060                             303                          647
## 280660                               0                            0
## 8225                              2396                         1803
## 90288                               18                            0
##           TCGA-VQ-A8PQ-01A-11R-A414-31 TCGA-VQ-A8PU-01A-12R-A414-31
## 100133144                           42                           71
## 100134869                           32                           52
## 155060                             590                          513
## 280660                               0                            0
## 8225                              1385                         1057
## 90288                               11                           61
##           TCGA-VQ-A8PX-01A-12R-A414-31 TCGA-VQ-A91A-01A-11R-A414-31
## 100133144                          167                           33
## 100134869                           91                           34
## 155060                             506                          782
## 280660                               0                            0
## 8225                              2196                          978
## 90288                               20                            6
##           TCGA-VQ-A91D-01A-11R-A414-31 TCGA-VQ-A91E-01A-31R-A414-31
## 100133144                          210                          191
## 100134869                          106                           91
## 155060                             976                          638
## 280660                               0                            0
## 8225                              1507                         1507
## 90288                               43                          151
##           TCGA-VQ-A91K-01A-11R-A414-31 TCGA-VQ-A91N-01A-11R-A414-31
## 100133144                          122                          120
## 100134869                           57                           52
## 155060                             364                          390
## 280660                               0                            0
## 8225                              1365                         1539
## 90288                               13                           51
##           TCGA-VQ-A91Q-01A-12R-A414-31 TCGA-VQ-A91S-01A-11R-A414-31
## 100133144                          102                           83
## 100134869                           72                           17
## 155060                             370                          408
## 280660                               0                            0
## 8225                              1287                         1288
## 90288                               12                           43
##           TCGA-VQ-A91U-01A-11R-A414-31 TCGA-VQ-A91V-01A-11R-A414-31
## 100133144                           50                          130
## 100134869                           54                           54
## 155060                             548                          561
## 280660                               0                            0
## 8225                              1478                         1334
## 90288                                5                           68
##           TCGA-VQ-A91W-01A-11R-A414-31 TCGA-VQ-A91X-01A-12R-A414-31
## 100133144                          139                          134
## 100134869                          103                           48
## 155060                             471                          858
## 280660                               0                            0
## 8225                              1670                         1859
## 90288                               77                           16
##           TCGA-VQ-A91Y-01A-11R-A414-31 TCGA-VQ-A91Z-01A-11R-A414-31
## 100133144                           35                          108
## 100134869                           15                           86
## 155060                             431                          608
## 280660                               0                            0
## 8225                               761                          530
## 90288                                5                          197
##           TCGA-VQ-A922-01A-11R-A414-31 TCGA-VQ-A923-01A-11R-A414-31
## 100133144                          112                          131
## 100134869                           52                           67
## 155060                             423                         1096
## 280660                               0                            0
## 8225                               627                         1120
## 90288                               16                           19
##           TCGA-VQ-A924-01A-11R-A414-31 TCGA-VQ-A925-01A-11R-A414-31
## 100133144                          137                           76
## 100134869                           68                           57
## 155060                             396                          506
## 280660                               0                            0
## 8225                              1605                         2319
## 90288                                1                          176
##           TCGA-VQ-A927-01A-12R-A414-31 TCGA-VQ-A928-01A-11R-A414-31
## 100133144                           97                           92
## 100134869                           48                           53
## 155060                             444                          780
## 280660                               0                            0
## 8225                              1506                         1407
## 90288                               23                          481
##           TCGA-VQ-A92D-01A-11R-A414-31 TCGA-VQ-A94O-01A-11R-A414-31
## 100133144                          113                           56
## 100134869                          110                           49
## 155060                             263                          338
## 280660                               0                            0
## 8225                               641                         1074
## 90288                               38                           42
##           TCGA-VQ-A94P-01A-13R-A414-31 TCGA-VQ-A94R-01A-11R-A414-31
## 100133144                           38                          146
## 100134869                           15                           50
## 155060                             270                          607
## 280660                               0                            1
## 8225                              1426                         1331
## 90288                                2                           24
##           TCGA-VQ-A94T-01A-11R-A414-31 TCGA-VQ-A94U-01A-12R-A414-31
## 100133144                           89                           79
## 100134869                           81                           64
## 155060                             358                          608
## 280660                               0                            0
## 8225                               808                         1279
## 90288                               18                           27
##           TCGA-VQ-AA64-01A-11R-A414-31 TCGA-VQ-AA68-01A-11R-A414-31
## 100133144                           74                          104
## 100134869                           55                           78
## 155060                             259                          296
## 280660                               0                            0
## 8225                               879                          775
## 90288                              132                           15
##           TCGA-VQ-AA69-01A-11R-A414-31 TCGA-VQ-AA6A-01A-11R-A414-31
## 100133144                          255                           83
## 100134869                          152                           39
## 155060                             628                          481
## 280660                               0                            0
## 8225                              1437                          896
## 90288                               13                           41
##           TCGA-VQ-AA6B-01A-11R-A414-31 TCGA-VQ-AA6D-01A-11R-A414-31
## 100133144                          128                          117
## 100134869                           72                           73
## 155060                             948                          435
## 280660                               0                            0
## 8225                              2559                         3326
## 90288                               13                           10
##           TCGA-VQ-AA6F-01A-31R-A414-31 TCGA-VQ-AA6G-01A-11R-A414-31
## 100133144                           54                          154
## 100134869                           42                           84
## 155060                             370                          270
## 280660                               0                            0
## 8225                              1049                          964
## 90288                              244                            9
##           TCGA-VQ-AA6I-01A-11R-A414-31 TCGA-VQ-AA6J-01A-11R-A414-31
## 100133144                          132                           72
## 100134869                           98                           48
## 155060                             228                          214
## 280660                               0                            0
## 8225                              2356                         1448
## 90288                               21                           27
##           TCGA-VQ-AA6K-01A-11R-A414-31 TCGA-ZA-A8F6-01A-23R-A36D-31
## 100133144                           76                           55
## 100134869                           51                           30
## 155060                             539                          337
## 280660                               0                            0
## 8225                              1810                         1638
## 90288                               52                            7
##           TCGA-ZQ-A9CR-01A-11R-A39E-31
## 100133144                           65
## 100134869                           25
## 155060                             205
## 280660                               0
## 8225                               960
## 90288                               12
# quantile filter of genes
dataFilt <- TCGAanalyze_Filtering(tabDF = dataNorm,
                                  method = "quantile",
                                  qnt.cut =  0.25)
write.csv(dataFilt,"dataFilt TCGA only tumor.csv")

#check clinical
rse$age_at_index
##   [1] 74 58 54 53 53 67 56 59 70 78 75 86 59 81 69 78 75 70 71 67 41 82 56 53 66
##  [26] 60 62 57 63 78 76 63 78 63 67 75 53 59 74 73 84 65 75 68 57 65 58 83 64 76
##  [51] 72 76 64 55 64 72 62 61 73 63 66 62 45 87 68 62 70 49 69 62 45 69 69 54 68
##  [76] 49 80 64 69 82 75 66 49 69 57 39 59 68 82 77 49 70 76 72 51 66 60 65 47 59
## [101] 79 68 69 79 62 52 58 72 71 51 51 72 70 69 63 72 67 83 50 51 78 58 62 70 50
## [126] 54 60 78 67 76 74 70 71 NA 72 58 57 60 70 71 61 71 79 76 73 46 77 62 71 54
## [151] 63 68 53 62 65 53 76 66 75 58 67 70 72 70 43 53 57 79 71 44 58 51 60 69 74
## [176] 48 58 78 81 72 86 90 51 55 56 65 58 54 86 48 68 52 80 71 79 74 75 76 66 69
## [201] 57 76 65 70 69 70 69 74 70 79 49 78 67 54 68 66 41 70 60 68 NA 72 71 63 65
## [226] 64 75 74 73 77 58 61 66 57 69 72 84 68 71 68 61 75 63 62 63 61 56 61 67 56
## [251] 68 57 80 58 77 64 56 72 56 56 73 69 81 78 42 90 59 78 63 79 59 51 74 73 60
## [276] NA 80 73 77 67 66 68 70 90 60 68 68 75 70 72 82 35 84 80 34 74 65 57 56 65
## [301] 58 69 76 72 90 68 72 57 64 66 74 79 48 70 54 65 78 72 67 55 76 53 72 52 67
## [326] 45 83 57 59 67 55 79 43 68 79 69 66 74 70 71 72 45 55 58 63 73 78 67 72 71
## [351] 59 45 66 72 74 73 59 64 61 58 45 56 59 58 78 57 69 51 30 68 75 70 53 65 NA
## [376] 69 52 51 51 74 84 74 NA 70 52 71 70 77 62 48 61 60 46 43 71 61 85 77 75 60
## [401] 80 58 70 63 81 77 63 68 58 51 56 90 44 50 59
rse$definition
##   [1] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##   [4] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##   [7] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [10] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [13] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [16] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [19] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [22] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [25] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [28] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [31] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [34] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [37] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [40] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [43] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [46] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [49] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [52] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [55] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [58] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [61] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [64] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [67] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [70] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [73] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [76] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [79] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [82] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [85] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [88] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [91] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [94] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
##  [97] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [100] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [103] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [106] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [109] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [112] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [115] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [118] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [121] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [124] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [127] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [130] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [133] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [136] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [139] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [142] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [145] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [148] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [151] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [154] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [157] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [160] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [163] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [166] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [169] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [172] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [175] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [178] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [181] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [184] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [187] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [190] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [193] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [196] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [199] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [202] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [205] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [208] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [211] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [214] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [217] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [220] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [223] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [226] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [229] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [232] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [235] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [238] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [241] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [244] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [247] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [250] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [253] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [256] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [259] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [262] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [265] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [268] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [271] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [274] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [277] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [280] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [283] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [286] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [289] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [292] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [295] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [298] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [301] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [304] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [307] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [310] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [313] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [316] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [319] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [322] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [325] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [328] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [331] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [334] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [337] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [340] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [343] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [346] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [349] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [352] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [355] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [358] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [361] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [364] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [367] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [370] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [373] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [376] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [379] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [382] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [385] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [388] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [391] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [394] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [397] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [400] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [403] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [406] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [409] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [412] "Primary solid Tumor" "Primary solid Tumor" "Primary solid Tumor"
## [415] "Primary solid Tumor"
rse$days_to_diagnosis
##   [1]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [26]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [51]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
##  [76]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## [101]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## [126]  0  0  0  0  0  0  0  0 NA  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## [151]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## [176]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## [201]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0 NA  0  0  0  0
## [226]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## [251]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## [276] NA  0  0  0  0  0  0  0  0  0  0  0 NA  0  0  0  0  0  0  0  0  0  0  0  0
## [301]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## [326]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## [351]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0 NA
## [376]  0  0  0  0  0  0  0 NA  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
## [401]  0  0  0  0  0  0  0  0  0  0  0  0  0  0  0
rse$ajcc_pathologic_stage
##   [1] "Stage II"   "Stage IIIB" "Stage IIB"  "Stage IIB"  "Stage IIIB"
##   [6] "Stage IV"   "Stage IIIC" "Stage IIB"  "Stage IIIC" "Stage IIA" 
##  [11] "Stage IIIB" "Stage IIIA" "Stage IIIB" "Stage II"   "Stage II"  
##  [16] NA           "Stage IIIB" "Stage IIB"  NA           "Stage IIIB"
##  [21] "Stage IV"   "Stage II"   NA           "Stage IIIB" "Stage IIIA"
##  [26] "Stage IIIB" "Stage IB"   "Stage IIB"  "Stage IIIB" "Stage IIIA"
##  [31] "Stage IIB"  "Stage IIIA" "Stage IIIA" "Stage IB"   "Stage IIB" 
##  [36] "Stage IIIA" "Stage II"   "Stage IIIA" "Stage IIIB" "Stage IIIB"
##  [41] NA           "Stage IIIC" "Stage IA"   "Stage IB"   "Stage IIA" 
##  [46] "Stage II"   "Stage IIB"  "Stage II"   "Stage IIB"  "Stage IA"  
##  [51] "Stage III"  "Stage IIIB" "Stage IV"   "Stage IIIC" "Stage IIA" 
##  [56] "Stage IIIA" "Stage IIB"  "Stage IB"   NA           NA          
##  [61] "Stage IIA"  "Stage IIIB" "Stage IV"   NA           "Stage IIIB"
##  [66] "Stage IIIC" "Stage IIIC" "Stage IV"   "Stage II"   "Stage II"  
##  [71] "Stage IIIA" "Stage IV"   "Stage IIIC" "Stage IIIB" "Stage IIA" 
##  [76] "Stage IIB"  "Stage IIIA" "Stage IV"   "Stage IIA"  "Stage IB"  
##  [81] "Stage IIIA" "Stage IIIA" "Stage IV"   "Stage IIIC" NA          
##  [86] "Stage IIIB" "Stage IV"   "Stage IIIA" "Stage IIA"  "Stage IB"  
##  [91] "Stage II"   "Stage IIIB" "Stage IIIA" "Stage IIB"  "Stage II"  
##  [96] "Stage IV"   "Stage II"   "Stage IIIA" "Stage IIIB" "Stage IIIB"
## [101] "Stage IB"   "Stage IIB"  "Stage IIIB" "Stage IA"   "Stage IB"  
## [106] "Stage II"   "Stage IB"   "Stage IIIB" "Stage IB"   "Stage IIIA"
## [111] "Stage IB"   "Stage IIIC" "Stage IIB"  "Stage IIIC" "Stage IV"  
## [116] "Stage II"   "Stage IIIA" "Stage IIIA" "Stage IIB"  "Stage IV"  
## [121] "Stage III"  NA           "Stage IIIB" "Stage IV"   "Stage IV"  
## [126] "Stage IIA"  NA           "Stage IIA"  "Stage IIA"  "Stage IIIA"
## [131] NA           "Stage IIIB" "Stage IIB"  "Stage IV"   "Stage IIB" 
## [136] "Stage IIIC" "Stage IB"   "Stage IIIC" "Stage IIIB" "Stage IB"  
## [141] "Stage IIIB" "Stage IIB"  "Stage IIIC" "Stage IIIA" "Stage IA"  
## [146] "Stage IIIA" "Stage IIIC" "Stage IIB"  "Stage IIB"  "Stage IIIB"
## [151] "Stage IA"   "Stage IIIB" "Stage IIIA" "Stage IIB"  "Stage IV"  
## [156] "Stage IIIA" "Stage IV"   NA           "Stage IV"   "Stage IIIB"
## [161] "Stage IIIC" "Stage IIA"  "Stage IIIA" "Stage IIIB" "Stage IIIA"
## [166] "Stage IV"   "Stage IIB"  "Stage IIIC" "Stage IIIB" "Stage IV"  
## [171] "Stage IIIA" "Stage IIB"  "Stage IIB"  "Stage IIIA" "Stage IIB" 
## [176] "Stage IIIA" "Stage IIB"  "Stage II"   "Stage IIIB" "Stage IIIA"
## [181] "Stage IV"   "Stage I"    "Stage IV"   "Stage IIA"  "Stage IIIB"
## [186] NA           "Stage IIIA" "Stage IB"   "Stage IIA"  "Stage IB"  
## [191] "Stage IIIA" "Stage IIIA" "Stage IIB"  "Stage IIIC" "Stage IIA" 
## [196] "Stage IA"   "Stage IIB"  "Stage IIIB" "Stage IIIA" "Stage IIB" 
## [201] "Stage IV"   "Stage IB"   "Stage IV"   "Stage IIA"  "Stage IIIB"
## [206] "Stage III"  "Stage II"   "Stage IIIC" "Stage IB"   "Stage IIB" 
## [211] "Stage IB"   "Stage IIIB" "Stage IIIB" "Stage IIA"  "Stage IIIA"
## [216] "Stage IIIC" "Stage II"   "Stage IV"   "Stage IIIC" "Stage IB"  
## [221] "Stage IIIA" NA           "Stage IB"   "Stage IIIB" "Stage IIIA"
## [226] NA           "Stage IIIB" "Stage IIB"  "Stage IIIB" "Stage IIIC"
## [231] "Stage IV"   "Stage IIIA" "Stage IV"   "Stage IIA"  "Stage IIA" 
## [236] "Stage IIIA" "Stage IB"   "Stage IIB"  "Stage IIIC" "Stage IIIA"
## [241] "Stage II"   NA           "Stage IIIA" "Stage IIIA" "Stage IIIC"
## [246] "Stage IIA"  "Stage IIIB" "Stage IIB"  "Stage IV"   "Stage IIIC"
## [251] "Stage IIIC" "Stage IIIB" "Stage IIA"  "Stage IB"   "Stage IB"  
## [256] "Stage IIA"  "Stage IV"   "Stage IV"   "Stage IV"   NA          
## [261] "Stage IIIA" "Stage IIIA" "Stage IA"   "Stage IIIA" "Stage IIIC"
## [266] "Stage IV"   "Stage IV"   "Stage II"   "Stage II"   "Stage IB"  
## [271] "Stage IB"   "Stage IA"   "Stage IIIB" "Stage IIIA" "Stage IIB" 
## [276] "Stage IA"   "Stage IIIA" "Stage IB"   "Stage IA"   "Stage IIIA"
## [281] "Stage IIIA" "Stage IV"   "Stage IIB"  NA           "Stage IIB" 
## [286] "Stage IIA"  "Stage IIIA" "Stage IIIC" "Stage IV"   "Stage IIIC"
## [291] "Stage IIIA" "Stage IIIA" NA           "Stage IIIA" "Stage IIIA"
## [296] "Stage IIB"  NA           "Stage IIB"  "Stage IIB"  "Stage IIIA"
## [301] "Stage IIIA" "Stage II"   "Stage IIA"  "Stage IIIA" "Stage IIIA"
## [306] "Stage IIA"  "Stage IIA"  "Stage IIIA" "Stage IIA"  "Stage IIB" 
## [311] "Stage IIIB" NA           "Stage II"   "Stage IIIB" "Stage IV"  
## [316] "Stage IIA"  "Stage II"   "Stage IIIB" "Stage IIIC" "Stage IIB" 
## [321] "Stage IIIA" "Stage IIIA" "Stage IIIB" "Stage IIB"  "Stage IIIC"
## [326] "Stage IIIB" "Stage II"   "Stage IIB"  "Stage IIIA" "Stage IB"  
## [331] "Stage IIA"  "Stage IIA"  "Stage II"   "Stage IIIB" "Stage IIB" 
## [336] "Stage IIB"  "Stage IV"   "Stage IIB"  "Stage IIA"  "Stage IIB" 
## [341] "Stage IB"   "Stage IIB"  "Stage IIIB" "Stage IIA"  "Stage IIB" 
## [346] "Stage IIB"  "Stage IV"   "Stage IA"   "Stage IB"   "Stage IIIB"
## [351] "Stage IV"   "Stage II"   "Stage IIIA" "Stage IIIC" NA          
## [356] "Stage IIB"  NA           "Stage IA"   "Stage IIIA" "Stage IIIB"
## [361] "Stage I"    "Stage IIIA" "Stage IIIC" "Stage IIA"  "Stage IIIA"
## [366] "Stage IIIB" "Stage IIA"  "Stage IIB"  "Stage IIIA" "Stage IB"  
## [371] "Stage IA"   "Stage IA"   "Stage IIA"  "Stage IIIA" "Stage II"  
## [376] "Stage IB"   "Stage IIIC" "Stage II"   "Stage IIIB" "Stage IIB" 
## [381] "Stage IB"   "Stage IIIB" "Stage IB"   "Stage IIIC" "Stage IIIC"
## [386] "Stage IIA"  "Stage IB"   NA           "Stage IIA"  "Stage IIIB"
## [391] "Stage IV"   "Stage IIB"  "Stage IIIA" "Stage IIIB" "Stage IB"  
## [396] "Stage IIA"  "Stage IB"   "Stage IB"   "Stage IIA"  "Stage IB"  
## [401] NA           "Stage IIIC" "Stage IIB"  "Stage IIIA" "Stage IB"  
## [406] "Stage IIIC" "Stage IIIA" "Stage IA"   "Stage II"   "Stage IIB" 
## [411] "Stage IIIA" "Stage IA"   "Stage IIIB" "Stage IV"   "Stage IIIA"
rse$tissue_or_organ_of_origin
##   [1] "Fundus of stomach"                "Body of stomach"                 
##   [3] "Gastric antrum"                   "Gastric antrum"                  
##   [5] "Gastric antrum"                   "Body of stomach"                 
##   [7] "Body of stomach"                  "Body of stomach"                 
##   [9] "Body of stomach"                  "Cardia, NOS"                     
##  [11] "Gastric antrum"                   "Gastric antrum"                  
##  [13] "Gastric antrum"                   "Gastric antrum"                  
##  [15] "Body of stomach"                  "Gastric antrum"                  
##  [17] "Gastric antrum"                   "Body of stomach"                 
##  [19] "Body of stomach"                  "Body of stomach"                 
##  [21] "Fundus of stomach"                "Gastric antrum"                  
##  [23] "Gastric antrum"                   "Fundus of stomach"               
##  [25] "Stomach, NOS"                     "Body of stomach"                 
##  [27] "Body of stomach"                  "Gastric antrum"                  
##  [29] "Body of stomach"                  "Gastric antrum"                  
##  [31] "Stomach, NOS"                     "Cardia, NOS"                     
##  [33] "Fundus of stomach"                "Fundus of stomach"               
##  [35] "Body of stomach"                  "Cardia, NOS"                     
##  [37] "Gastric antrum"                   "Cardia, NOS"                     
##  [39] "Cardia, NOS"                      "Fundus of stomach"               
##  [41] "Cardia, NOS"                      "Fundus of stomach"               
##  [43] "Body of stomach"                  "Fundus of stomach"               
##  [45] "Cardia, NOS"                      "Gastric antrum"                  
##  [47] "Gastric antrum"                   "Cardia, NOS"                     
##  [49] "Body of stomach"                  "Cardia, NOS"                     
##  [51] "Fundus of stomach"                "Gastric antrum"                  
##  [53] "Cardia, NOS"                      "Gastric antrum"                  
##  [55] "Cardia, NOS"                      "Body of stomach"                 
##  [57] "Cardia, NOS"                      "Gastric antrum"                  
##  [59] "Body of stomach"                  "Gastric antrum"                  
##  [61] "Stomach, NOS"                     "Cardia, NOS"                     
##  [63] "Gastric antrum"                   "Gastric antrum"                  
##  [65] "Cardia, NOS"                      "Fundus of stomach"               
##  [67] "Fundus of stomach"                "Gastric antrum"                  
##  [69] "Gastric antrum"                   "Cardia, NOS"                     
##  [71] "Gastric antrum"                   "Gastric antrum"                  
##  [73] "Body of stomach"                  "Cardia, NOS"                     
##  [75] "Cardia, NOS"                      "Gastric antrum"                  
##  [77] "Body of stomach"                  "Cardia, NOS"                     
##  [79] "Cardia, NOS"                      "Fundus of stomach"               
##  [81] "Fundus of stomach"                "Fundus of stomach"               
##  [83] "Body of stomach"                  "Gastric antrum"                  
##  [85] "Body of stomach"                  "Gastric antrum"                  
##  [87] "Gastric antrum"                   "Cardia, NOS"                     
##  [89] "Gastric antrum"                   "Gastric antrum"                  
##  [91] "Gastric antrum"                   "Gastric antrum"                  
##  [93] "Body of stomach"                  "Body of stomach"                 
##  [95] "Gastric antrum"                   "Cardia, NOS"                     
##  [97] "Body of stomach"                  "Body of stomach"                 
##  [99] "Gastric antrum"                   "Body of stomach"                 
## [101] "Cardia, NOS"                      "Gastric antrum"                  
## [103] "Cardia, NOS"                      "Gastric antrum"                  
## [105] "Fundus of stomach"                "Cardia, NOS"                     
## [107] "Gastric antrum"                   "Gastric antrum"                  
## [109] "Body of stomach"                  "Fundus of stomach"               
## [111] "Body of stomach"                  "Body of stomach"                 
## [113] "Gastric antrum"                   "Body of stomach"                 
## [115] "Cardia, NOS"                      "Gastric antrum"                  
## [117] "Body of stomach"                  "Body of stomach"                 
## [119] "Cardia, NOS"                      "Gastric antrum"                  
## [121] "Stomach, NOS"                     "Body of stomach"                 
## [123] "Gastric antrum"                   "Gastric antrum"                  
## [125] "Body of stomach"                  "Body of stomach"                 
## [127] "Body of stomach"                  "Body of stomach"                 
## [129] "Body of stomach"                  "Stomach, NOS"                    
## [131] "Stomach, NOS"                     "Gastric antrum"                  
## [133] "Gastric antrum"                   "Stomach, NOS"                    
## [135] "Fundus of stomach"                "Body of stomach"                 
## [137] "Stomach, NOS"                     "Body of stomach"                 
## [139] "Body of stomach"                  "Fundus of stomach"               
## [141] "Gastric antrum"                   "Gastric antrum"                  
## [143] "Gastric antrum"                   "Gastric antrum"                  
## [145] "Gastric antrum"                   "Cardia, NOS"                     
## [147] "Body of stomach"                  "Body of stomach"                 
## [149] "Body of stomach"                  "Gastric antrum"                  
## [151] "Cardia, NOS"                      "Cardia, NOS"                     
## [153] "Body of stomach"                  "Cardia, NOS"                     
## [155] "Gastric antrum"                   "Cardia, NOS"                     
## [157] "Body of stomach"                  "Cardia, NOS"                     
## [159] "Cardia, NOS"                      "Cardia, NOS"                     
## [161] "Gastric antrum"                   "Gastric antrum"                  
## [163] "Gastric antrum"                   "Body of stomach"                 
## [165] "Gastric antrum"                   "Body of stomach"                 
## [167] "Fundus of stomach"                "Gastric antrum"                  
## [169] "Cardia, NOS"                      "Stomach, NOS"                    
## [171] "Cardia, NOS"                      "Body of stomach"                 
## [173] "Gastric antrum"                   "Gastric antrum"                  
## [175] "Cardia, NOS"                      "Gastric antrum"                  
## [177] "Gastric antrum"                   "Cardia, NOS"                     
## [179] "Body of stomach"                  "Gastric antrum"                  
## [181] "Gastric antrum"                   "Gastric antrum"                  
## [183] "Cardia, NOS"                      "Fundus of stomach"               
## [185] "Fundus of stomach"                "Body of stomach"                 
## [187] "Gastric antrum"                   "Body of stomach"                 
## [189] "Gastric antrum"                   "Gastric antrum"                  
## [191] "Body of stomach"                  "Gastric antrum"                  
## [193] "Cardia, NOS"                      "Fundus of stomach"               
## [195] "Cardia, NOS"                      "Cardia, NOS"                     
## [197] "Cardia, NOS"                      "Body of stomach"                 
## [199] "Gastric antrum"                   "Gastric antrum"                  
## [201] "Body of stomach"                  "Fundus of stomach"               
## [203] "Gastric antrum"                   "Fundus of stomach"               
## [205] "Gastric antrum"                   "Body of stomach"                 
## [207] "Gastric antrum"                   "Gastric antrum"                  
## [209] "Lesser curvature of stomach, NOS" "Body of stomach"                 
## [211] "Gastric antrum"                   "Cardia, NOS"                     
## [213] "Gastric antrum"                   "Body of stomach"                 
## [215] "Body of stomach"                  "Body of stomach"                 
## [217] "Gastric antrum"                   "Stomach, NOS"                    
## [219] "Gastric antrum"                   "Cardia, NOS"                     
## [221] "Cardia, NOS"                      "Stomach, NOS"                    
## [223] "Cardia, NOS"                      "Fundus of stomach"               
## [225] "Cardia, NOS"                      "Cardia, NOS"                     
## [227] "Cardia, NOS"                      "Fundus of stomach"               
## [229] "Cardia, NOS"                      "Fundus of stomach"               
## [231] "Gastric antrum"                   "Fundus of stomach"               
## [233] "Body of stomach"                  "Fundus of stomach"               
## [235] "Body of stomach"                  "Body of stomach"                 
## [237] "Cardia, NOS"                      "Cardia, NOS"                     
## [239] "Gastric antrum"                   "Cardia, NOS"                     
## [241] "Gastric antrum"                   "Cardia, NOS"                     
## [243] "Gastric antrum"                   "Gastric antrum"                  
## [245] "Fundus of stomach"                "Gastric antrum"                  
## [247] "Body of stomach"                  "Gastric antrum"                  
## [249] "Gastric antrum"                   "Cardia, NOS"                     
## [251] "Fundus of stomach"                "Body of stomach"                 
## [253] "Fundus of stomach"                "Cardia, NOS"                     
## [255] "Cardia, NOS"                      "Gastric antrum"                  
## [257] "Gastric antrum"                   "Stomach, NOS"                    
## [259] "Cardia, NOS"                      "Gastric antrum"                  
## [261] "Gastric antrum"                   "Gastric antrum"                  
## [263] "Body of stomach"                  "Gastric antrum"                  
## [265] "Fundus of stomach"                "Gastric antrum"                  
## [267] "Cardia, NOS"                      "Gastric antrum"                  
## [269] "Cardia, NOS"                      "Cardia, NOS"                     
## [271] "Gastric antrum"                   "Stomach, NOS"                    
## [273] "Gastric antrum"                   "Fundus of stomach"               
## [275] "Body of stomach"                  "Body of stomach"                 
## [277] "Body of stomach"                  "Gastric antrum"                  
## [279] "Body of stomach"                  "Gastric antrum"                  
## [281] "Cardia, NOS"                      "Body of stomach"                 
## [283] "Gastric antrum"                   "Pylorus"                         
## [285] "Fundus of stomach"                "Cardia, NOS"                     
## [287] "Body of stomach"                  "Gastric antrum"                  
## [289] "Gastric antrum"                   "Gastric antrum"                  
## [291] "Gastric antrum"                   "Cardia, NOS"                     
## [293] "Cardia, NOS"                      "Cardia, NOS"                     
## [295] "Gastric antrum"                   "Body of stomach"                 
## [297] "Body of stomach"                  "Cardia, NOS"                     
## [299] "Gastric antrum"                   "Gastric antrum"                  
## [301] "Cardia, NOS"                      "Gastric antrum"                  
## [303] "Cardia, NOS"                      "Gastric antrum"                  
## [305] "Body of stomach"                  "Stomach, NOS"                    
## [307] "Cardia, NOS"                      "Gastric antrum"                  
## [309] "Body of stomach"                  "Gastric antrum"                  
## [311] "Gastric antrum"                   "Gastric antrum"                  
## [313] "Gastric antrum"                   "Gastric antrum"                  
## [315] "Body of stomach"                  "Body of stomach"                 
## [317] "Body of stomach"                  "Gastric antrum"                  
## [319] "Cardia, NOS"                      "Fundus of stomach"               
## [321] "Body of stomach"                  "Gastric antrum"                  
## [323] "Gastric antrum"                   "Gastric antrum"                  
## [325] "Gastric antrum"                   "Gastric antrum"                  
## [327] "Cardia, NOS"                      "Body of stomach"                 
## [329] "Gastric antrum"                   "Cardia, NOS"                     
## [331] "Gastric antrum"                   "Gastric antrum"                  
## [333] "Stomach, NOS"                     "Body of stomach"                 
## [335] "Gastric antrum"                   "Cardia, NOS"                     
## [337] "Fundus of stomach"                "Body of stomach"                 
## [339] "Body of stomach"                  "Gastric antrum"                  
## [341] "Gastric antrum"                   "Gastric antrum"                  
## [343] "Fundus of stomach"                "Cardia, NOS"                     
## [345] "Fundus of stomach"                "Cardia, NOS"                     
## [347] "Gastric antrum"                   "Body of stomach"                 
## [349] "Cardia, NOS"                      "Cardia, NOS"                     
## [351] "Gastric antrum"                   "Gastric antrum"                  
## [353] "Fundus of stomach"                "Body of stomach"                 
## [355] "Gastric antrum"                   "Gastric antrum"                  
## [357] "Cardia, NOS"                      "Cardia, NOS"                     
## [359] "Cardia, NOS"                      "Gastric antrum"                  
## [361] "Cardia, NOS"                      "Cardia, NOS"                     
## [363] "Cardia, NOS"                      "Gastric antrum"                  
## [365] "Cardia, NOS"                      "Cardia, NOS"                     
## [367] "Gastric antrum"                   "Fundus of stomach"               
## [369] "Body of stomach"                  "Cardia, NOS"                     
## [371] "Body of stomach"                  "Cardia, NOS"                     
## [373] "Cardia, NOS"                      "Fundus of stomach"               
## [375] "Gastric antrum"                   "Body of stomach"                 
## [377] "Fundus of stomach"                "Fundus of stomach"               
## [379] "Stomach, NOS"                     "Gastric antrum"                  
## [381] "Fundus of stomach"                "Gastric antrum"                  
## [383] "Stomach, NOS"                     "Gastric antrum"                  
## [385] "Cardia, NOS"                      "Gastric antrum"                  
## [387] "Body of stomach"                  "Cardia, NOS"                     
## [389] "Gastric antrum"                   "Cardia, NOS"                     
## [391] "Cardia, NOS"                      "Gastric antrum"                  
## [393] "Body of stomach"                  "Body of stomach"                 
## [395] "Gastric antrum"                   "Stomach, NOS"                    
## [397] "Gastric antrum"                   "Body of stomach"                 
## [399] "Body of stomach"                  "Fundus of stomach"               
## [401] "Gastric antrum"                   "Body of stomach"                 
## [403] "Body of stomach"                  "Body of stomach"                 
## [405] "Cardia, NOS"                      "Gastric antrum"                  
## [407] "Gastric antrum"                   "Body of stomach"                 
## [409] "Cardia, NOS"                      "Gastric antrum"                  
## [411] "Gastric antrum"                   "Fundus of stomach"               
## [413] "Cardia, NOS"                      "Cardia, NOS"                     
## [415] "Fundus of stomach"
rse$days_to_last_follow_up
##   [1]  378   21  170  725 1133   30  882  399   NA  411   18  600  229  580 1072
##  [16]    0  352  900    0 1200   NA  408   46 1236    0  899  356   NA 1000   NA
##  [31]  699  402   NA    0   19  582  543 1010   77  500   NA   11   23   NA  378
##  [46] 1023  392 2496  344  383   25  427  666   21 1367  820    5  579    0   NA
##  [61]  131   11  972    0   NA   65    0  365  485  126  176   NA    0  325  104
##  [76]  989  385  198   20   NA    7  383   NA  113   NA   16   NA   17  694  428
##  [91]  895  647  881  942  400 1674   12  940  411  564  440  268  356   NA  476
## [106]    3  566   35   NA  288    0   64  431   NA   21    2  523   NA 1106   92
## [121]    0    0   NA  262   21  485    0 1055   NA    0    0   35  342 1918  628
## [136]  225  243    7  641  724  419  237  856    8   NA   NA  678 1210  981  212
## [151]  479   NA  376  413  374  376   NA    0   92   NA   NA  415  344 3519  375
## [166]   NA  511   NA  411 2267 1297  812 1190 1862   29   NA  679 1124   NA  644
## [181]    0    0 1389  337  825  564 2171 1935  371   NA   NA  521  572  946  519
## [196]  738   40   NA   NA  180    8  754   NA   90  477   NA  280   NA 1765 1145
## [211]   NA  422  664  949   NA   NA  367   NA  650  613   NA    0   NA    6  156
## [226]  625  838  335   NA   28  183   22   NA  593  416 1132   NA   NA   NA   47
## [241]  388    0   NA    3  951  912 3720  496    0 1184  280 1319   29  942   12
## [256]   34 1645   NA   NA    0 1016   15 1100   NA  675   NA 1138    2 1083  678
## [271] 3540 1964   NA  381   47 1588    0   NA  742 1690   NA   NA  819    0  287
## [286]   NA 1160  928   NA   22  383  864  158   NA  838  574    0 1646  692   NA
## [301]  181   NA    2  523   NA  346  594   20  997  636  813    0  468  494   31
## [316] 1023   31 1153   19  389 1431  573   NA  991  482   24  245  213  164 2032
## [331]   14   NA    0  421    4  594   NA  308 1223  690  643  739  418    0 1108
## [346]  323    0  736   NA   NA   NA  396  618   15    0  200   NA  379  607  394
## [361]  559  434   NA    4   NA   38  785  224 1851  621  358   NA 1038  450 2351
## [376] 1090  595  377   NA   NA  131   99   NA  616 1328  198  463  189  273 1002
## [391]   NA  449   25 1484  525  427    0  375  491  384    0   45  486  389  577
## [406]   92   NA  912   NA  374  862    0  752   NA  390
rse$primary_diagnosis
##   [1] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
##   [3] "Tubular adenocarcinoma"             "Tubular adenocarcinoma"            
##   [5] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
##   [7] "Carcinoma, diffuse type"            "Adenocarcinoma, NOS"               
##   [9] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
##  [11] "Tubular adenocarcinoma"             "Tubular adenocarcinoma"            
##  [13] "Adenocarcinoma, intestinal type"    "Mucinous adenocarcinoma"           
##  [15] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
##  [17] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
##  [19] "Adenocarcinoma, NOS"                "Mucinous adenocarcinoma"           
##  [21] "Carcinoma, diffuse type"            "Mucinous adenocarcinoma"           
##  [23] "Tubular adenocarcinoma"             "Carcinoma, diffuse type"           
##  [25] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
##  [27] "Carcinoma, diffuse type"            "Carcinoma, diffuse type"           
##  [29] "Tubular adenocarcinoma"             "Adenocarcinoma, intestinal type"   
##  [31] "Adenocarcinoma with mixed subtypes" "Adenocarcinoma, NOS"               
##  [33] "Mucinous adenocarcinoma"            "Adenocarcinoma, NOS"               
##  [35] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
##  [37] "Carcinoma, diffuse type"            "Mucinous adenocarcinoma"           
##  [39] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
##  [41] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
##  [43] "Tubular adenocarcinoma"             "Carcinoma, diffuse type"           
##  [45] "Adenocarcinoma, NOS"                "Papillary adenocarcinoma, NOS"     
##  [47] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
##  [49] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
##  [51] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
##  [53] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
##  [55] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
##  [57] "Adenocarcinoma, NOS"                "Signet ring cell carcinoma"        
##  [59] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
##  [61] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
##  [63] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
##  [65] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
##  [67] "Adenocarcinoma, NOS"                "Adenocarcinoma with mixed subtypes"
##  [69] "Adenocarcinoma, NOS"                "Papillary adenocarcinoma, NOS"     
##  [71] "Mucinous adenocarcinoma"            "Carcinoma, diffuse type"           
##  [73] "Carcinoma, diffuse type"            "Adenocarcinoma, NOS"               
##  [75] "Adenocarcinoma, NOS"                "Mucinous adenocarcinoma"           
##  [77] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
##  [79] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
##  [81] "Tubular adenocarcinoma"             "Carcinoma, diffuse type"           
##  [83] "Papillary adenocarcinoma, NOS"      "Adenocarcinoma, NOS"               
##  [85] "Signet ring cell carcinoma"         "Adenocarcinoma, NOS"               
##  [87] "Tubular adenocarcinoma"             "Adenocarcinoma, intestinal type"   
##  [89] "Tubular adenocarcinoma"             "Tubular adenocarcinoma"            
##  [91] "Adenocarcinoma, NOS"                "Mucinous adenocarcinoma"           
##  [93] "Tubular adenocarcinoma"             "Adenocarcinoma, intestinal type"   
##  [95] "Papillary adenocarcinoma, NOS"      "Adenocarcinoma, intestinal type"   
##  [97] "Mucinous adenocarcinoma"            "Adenocarcinoma, NOS"               
##  [99] "Carcinoma, diffuse type"            "Adenocarcinoma, NOS"               
## [101] "Adenocarcinoma, intestinal type"    "Carcinoma, diffuse type"           
## [103] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [105] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
## [107] "Carcinoma, diffuse type"            "Adenocarcinoma, NOS"               
## [109] "Signet ring cell carcinoma"         "Adenocarcinoma, intestinal type"   
## [111] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [113] "Carcinoma, diffuse type"            "Adenocarcinoma, NOS"               
## [115] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [117] "Tubular adenocarcinoma"             "Adenocarcinoma, intestinal type"   
## [119] "Carcinoma, diffuse type"            "Signet ring cell carcinoma"        
## [121] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [123] "Tubular adenocarcinoma"             "Tubular adenocarcinoma"            
## [125] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [127] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [129] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [131] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [133] "Adenocarcinoma, NOS"                "Mucinous adenocarcinoma"           
## [135] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [137] "Adenocarcinoma, intestinal type"    "Signet ring cell carcinoma"        
## [139] "Carcinoma, diffuse type"            "Papillary adenocarcinoma, NOS"     
## [141] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [143] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [145] "Adenocarcinoma, intestinal type"    "Carcinoma, diffuse type"           
## [147] "Carcinoma, diffuse type"            "Adenocarcinoma, NOS"               
## [149] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
## [151] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [153] "Carcinoma, diffuse type"            "Adenocarcinoma, NOS"               
## [155] "Mucinous adenocarcinoma"            "Tubular adenocarcinoma"            
## [157] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
## [159] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [161] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
## [163] "Tubular adenocarcinoma"             "Carcinoma, diffuse type"           
## [165] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
## [167] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
## [169] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [171] "Tubular adenocarcinoma"             "Carcinoma, diffuse type"           
## [173] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [175] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [177] "Carcinoma, diffuse type"            "Carcinoma, diffuse type"           
## [179] "Carcinoma, diffuse type"            "Tubular adenocarcinoma"            
## [181] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [183] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
## [185] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [187] "Carcinoma, diffuse type"            "Adenocarcinoma, intestinal type"   
## [189] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [191] "Adenocarcinoma, intestinal type"    "Tubular adenocarcinoma"            
## [193] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [195] "Adenocarcinoma, NOS"                "Papillary adenocarcinoma, NOS"     
## [197] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
## [199] "Tubular adenocarcinoma"             "Tubular adenocarcinoma"            
## [201] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [203] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [205] "Tubular adenocarcinoma"             "Tubular adenocarcinoma"            
## [207] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [209] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
## [211] "Carcinoma, diffuse type"            "Tubular adenocarcinoma"            
## [213] "Adenocarcinoma, intestinal type"    "Carcinoma, diffuse type"           
## [215] "Adenocarcinoma, intestinal type"    "Tubular adenocarcinoma"            
## [217] "Carcinoma, diffuse type"            "Adenocarcinoma, intestinal type"   
## [219] "Carcinoma, diffuse type"            "Signet ring cell carcinoma"        
## [221] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [223] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [225] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [227] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, intestinal type"   
## [229] "Carcinoma, diffuse type"            "Adenocarcinoma, NOS"               
## [231] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [233] "Adenocarcinoma, intestinal type"    "Tubular adenocarcinoma"            
## [235] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
## [237] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [239] "Tubular adenocarcinoma"             "Signet ring cell carcinoma"        
## [241] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [243] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
## [245] "Adenocarcinoma, intestinal type"    "Tubular adenocarcinoma"            
## [247] "Adenocarcinoma, intestinal type"    "Carcinoma, diffuse type"           
## [249] "Carcinoma, diffuse type"            "Adenocarcinoma, intestinal type"   
## [251] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
## [253] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [255] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [257] "Adenocarcinoma, intestinal type"    "Carcinoma, diffuse type"           
## [259] "Signet ring cell carcinoma"         "Adenocarcinoma, NOS"               
## [261] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
## [263] "Papillary adenocarcinoma, NOS"      "Carcinoma, diffuse type"           
## [265] "Carcinoma, diffuse type"            "Adenocarcinoma, NOS"               
## [267] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
## [269] "Carcinoma, diffuse type"            "Adenocarcinoma, intestinal type"   
## [271] "Carcinoma, diffuse type"            "Adenocarcinoma, intestinal type"   
## [273] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, intestinal type"   
## [275] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, intestinal type"   
## [277] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [279] "Tubular adenocarcinoma"             "Tubular adenocarcinoma"            
## [281] "Tubular adenocarcinoma"             "Adenocarcinoma, intestinal type"   
## [283] "Signet ring cell carcinoma"         "Adenocarcinoma, NOS"               
## [285] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, intestinal type"   
## [287] "Mucinous adenocarcinoma"            "Mucinous adenocarcinoma"           
## [289] "Signet ring cell carcinoma"         "Adenocarcinoma, intestinal type"   
## [291] "Mucinous adenocarcinoma"            "Adenocarcinoma, NOS"               
## [293] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [295] "Carcinoma, diffuse type"            "Adenocarcinoma, intestinal type"   
## [297] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
## [299] "Tubular adenocarcinoma"             "Signet ring cell carcinoma"        
## [301] "Carcinoma, diffuse type"            "Tubular adenocarcinoma"            
## [303] "Carcinoma, diffuse type"            "Adenocarcinoma, NOS"               
## [305] "Tubular adenocarcinoma"             "Adenocarcinoma, intestinal type"   
## [307] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
## [309] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [311] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [313] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [315] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [317] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, intestinal type"   
## [319] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [321] "Carcinoma, diffuse type"            "Tubular adenocarcinoma"            
## [323] "Tubular adenocarcinoma"             "Mucinous adenocarcinoma"           
## [325] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [327] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [329] "Adenocarcinoma, intestinal type"    "Tubular adenocarcinoma"            
## [331] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [333] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [335] "Adenocarcinoma, NOS"                "Mucinous adenocarcinoma"           
## [337] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [339] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [341] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [343] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [345] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [347] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
## [349] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [351] "Carcinoma, diffuse type"            "Adenocarcinoma, intestinal type"   
## [353] "Adenocarcinoma, intestinal type"    "Mucinous adenocarcinoma"           
## [355] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [357] "Carcinoma, diffuse type"            "Adenocarcinoma, NOS"               
## [359] "Adenocarcinoma, intestinal type"    "Tubular adenocarcinoma"            
## [361] "Adenocarcinoma, NOS"                "Tubular adenocarcinoma"            
## [363] "Signet ring cell carcinoma"         "Carcinoma, diffuse type"           
## [365] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [367] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
## [369] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [371] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
## [373] "Carcinoma, diffuse type"            "Adenocarcinoma, intestinal type"   
## [375] "Mucinous adenocarcinoma"            "Adenocarcinoma, NOS"               
## [377] "Carcinoma, diffuse type"            "Carcinoma, diffuse type"           
## [379] "Adenocarcinoma, NOS"                "Signet ring cell carcinoma"        
## [381] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [383] "Adenocarcinoma, NOS"                "Carcinoma, diffuse type"           
## [385] "Tubular adenocarcinoma"             "Tubular adenocarcinoma"            
## [387] "Tubular adenocarcinoma"             "Adenocarcinoma, NOS"               
## [389] "Carcinoma, diffuse type"            "Adenocarcinoma, intestinal type"   
## [391] "Tubular adenocarcinoma"             "Mucinous adenocarcinoma"           
## [393] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [395] "Adenocarcinoma, intestinal type"    "Adenocarcinoma, NOS"               
## [397] "Adenocarcinoma, intestinal type"    "Tubular adenocarcinoma"            
## [399] "Adenocarcinoma, NOS"                "Adenocarcinoma, NOS"               
## [401] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [403] "Tubular adenocarcinoma"             "Tubular adenocarcinoma"            
## [405] "Adenocarcinoma, intestinal type"    "Carcinoma, diffuse type"           
## [407] "Adenocarcinoma, NOS"                "Adenocarcinoma, intestinal type"   
## [409] "Adenocarcinoma, intestinal type"    "Carcinoma, diffuse type"           
## [411] "Mucinous adenocarcinoma"            "Adenocarcinoma, NOS"               
## [413] "Tubular adenocarcinoma"             "Tubular adenocarcinoma"            
## [415] "Adenocarcinoma, NOS"
rse$ajcc_pathologic_t
##   [1] "T3"  "T4b" "T2"  "T2"  "T4a" "T3"  "T4a" "T3"  "T4b" "T3"  "T4a" "T3" 
##  [13] "T3"  "T2"  "T3"  "TX"  "T3"  "T4a" "T2"  "T3"  "T4a" "T3"  "T3"  "T3" 
##  [25] "T4"  "T4b" "T2"  "T3"  "T4b" "T2"  "T3"  "T3"  "T3"  "T2"  "T4a" "T2" 
##  [37] "T2"  "T4a" "T3"  "T3"  "T3"  "T4b" "T1b" "T2"  "T3"  "T3"  "T4a" "T2" 
##  [49] "T2"  "T1b" "T4"  "T3"  "T3"  "T4a" "T3"  "T4a" "T3"  "T2"  "T1"  "T4a"
##  [61] "T3"  "T3"  "T4b" "TX"  "T3"  "T4b" "T4b" "T4"  "T2a" "T2"  "T3"  "T4" 
##  [73] "T4b" "T3"  "T3"  "T4a" "T3"  "T3"  "T3"  "T2"  "T3"  "T3"  "T3"  "T4b"
##  [85] "T4"  "T4a" "T4"  "T3"  "T3"  "T1b" "T3"  "T3"  "T3"  "T4a" "T3"  "T2" 
##  [97] "T3"  "T3"  "T4a" "T3"  "T2"  "T2"  "T3"  "T2"  "T2"  "T3"  "T2"  "T4a"
## [109] "T2b" "T4"  "T2a" "T4a" "T4a" "T4a" "T4"  "T2"  "T3"  "T2"  "T3"  "T4a"
## [121] "T2b" "T3"  "T3"  "T4"  "T3"  "T2"  "T3"  "T3"  "T3"  "T3"  "TX"  "T3" 
## [133] "T2"  "T2b" "T4a" "T4b" "T2"  "T4b" "T4a" "T2"  "T3"  "T3"  "T4a" "T4" 
## [145] "T1"  "T3"  "T4a" "T3"  "T4a" "T3"  "T1b" "T3"  "T2"  "T3"  "T4"  "T2" 
## [157] "T4"  "T2a" "T4"  "T3"  "T4a" "T3"  "T3"  "T3"  "T4"  "T4"  "T2"  "T4a"
## [169] "T3"  "T4"  "T3"  "T4a" "T3"  "T3"  "T3"  "T3"  "T4a" "T2b" "T3"  "T3" 
## [181] "T4a" "T1b" "T3"  "T3"  "T4b" "T2b" "T3"  "T1"  "T3"  "T2"  "T3"  "T4a"
## [193] "T2"  "T4b" "T3"  "T1b" "T2"  "T3"  "T3"  "T3"  "T4"  "T2"  "T4a" "T3" 
## [205] "T4b" "T3"  "T3"  "T4a" "T2b" "T3"  "T2a" "T3"  "T4b" "T3"  "T3"  "T4a"
## [217] "T3"  "T3"  "T4"  "T2"  "T3"  "TX"  "T2"  "T4b" "T3"  "T2"  "T4a" "T4a"
## [229] "T3"  "T4b" "T4"  "T4a" "T4"  "T3"  "T3"  "T4"  "T2a" "T2"  "T4b" "T3" 
## [241] "T3"  "TX"  "T3"  "T3"  "T4b" "T2"  "T3"  "T3"  "T4a" "T4"  "T4"  "T3" 
## [253] "T3"  "T2a" "T2"  "T3"  "T4"  "T3"  "T4"  "TX"  "T3"  "T3"  "T1b" "T3" 
## [265] "T4b" "T3"  "T3"  "T3"  "T2"  "T2"  "T2"  "T1"  "T3"  "T3"  "T4a" "T1" 
## [277] "T3"  "T2"  "T1a" "T3"  "T3"  "T3"  "T4a" "T3"  "T4a" "T3"  "T4a" "T4a"
## [289] "T4"  "T4a" "T3"  "T3"  "T2"  "T3"  "T4a" "T4a" "T2a" "T3"  "T3"  "T3" 
## [301] "T2"  "T3"  "T3"  "T2"  "T3"  "T3"  "T1b" "T4a" "T3"  "T2"  "T3"  "TX" 
## [313] "T3"  "T4b" "T4"  "T3"  "T2b" "T3"  "T4b" "T4a" "T2b" "T2b" "T3"  "T4a"
## [325] "T4b" "T4a" "T2"  "T3"  "T3"  "T2b" "T3"  "T3"  "T2a" "T3"  "T3"  "T3" 
## [337] "T3"  "T3"  "T3"  "T3"  "T2"  "T3"  "T3"  "T3"  "T3"  "T3"  "T4"  "T1a"
## [349] "T2"  "T3"  "T3"  "T2"  "T3"  "T4"  "TX"  "T3"  "T3"  "T1b" "T3"  "T3" 
## [361] "T1b" "T2"  "T4a" "T3"  "T3"  "T3"  "T3"  "T3"  "T3"  "T2"  "T1b" "T1b"
## [373] "T3"  "T4a" "T2b" "T2"  "T4"  "T3"  "T3"  "T4a" "T2"  "T4a" "T2b" "T4b"
## [385] "T4a" "T3"  "T2"  "T1b" "T2"  "T3"  "T3"  "T2"  "T3"  "T3"  "T2"  "T2" 
## [397] "T2"  "T2"  "T3"  "T2"  "TX"  "T4b" "T2"  "T2b" "T2a" "T4a" "T4a" "T1" 
## [409] "T2b" "T3"  "T4a" "T1b" "T3"  "T4"  "T3"
rse$ajcc_pathologic_n
##   [1] "N0"  "N1"  "N2"  "N2"  "N2"  "N2"  "N3b" "N1"  "N2"  "N0"  "N2"  "N2" 
##  [13] "N3a" "N1"  "N0"  "N1"  "N3a" "N0"  "NX"  "N3a" "N3"  "N0"  NA    "N2" 
##  [25] "N0"  "N0"  "N0"  "N1"  "N1"  "N2"  "N1"  "N1"  "N1"  "N0"  "N0"  "N3" 
##  [37] "N1"  "N1"  "N2"  "N3a" "N1"  "N3a" "N0"  "N0"  "N0"  "N0"  "N0"  "N1" 
##  [49] "N1"  "N0"  "N1"  "N3a" "N3a" "N3a" "N0"  "N1"  "N1"  "N0"  "NX"  "N2" 
##  [61] "N0"  "N3a" "N2"  "NX"  "N3"  "N2"  "N3a" "N1"  "N1"  "N1"  "N2"  "N3" 
##  [73] "N3a" "N3a" "N0"  "NX"  "N2"  "N3"  "N0"  "N0"  "N2"  "N1"  "N3"  "N2" 
##  [85] "NX"  "N2"  "N3"  "N2"  "N0"  "N1"  "N0"  "N3b" "N2"  "N0"  "N0"  "N3" 
##  [97] "N0"  "N2"  "N2"  "N3a" "N0"  "N2"  "N3"  "N0"  "N0"  "N0"  "N0"  "N2" 
## [109] "N0"  NA    "N0"  "N3b" "N0"  "N3"  "N1"  "N1"  "N2"  "N2"  "N1"  "N3a"
## [121] "N1"  "NX"  "N3"  "N1"  "N3a" "N1"  "NX"  "N0"  "N0"  "N1"  "N1"  "N3a"
## [133] "N2"  "N3"  "N0"  "N3a" "N0"  "N3a" "N2"  "N0"  "N3a" "N1"  "N3a" "N1" 
## [145] "N0"  "N1"  "N3a" "N1"  "N0"  "N3a" "N0"  "N2"  "N3"  "N1"  "N0"  "N3" 
## [157] "N1"  "NX"  "N1"  "N3a" "N3b" "N0"  "N2"  "N2"  "N0"  "N2"  "N2"  "N3" 
## [169] "N3a" "N1"  "N2"  "N0"  "N1"  "N1"  "N1"  "N1"  "N0"  "N1"  "N3"  "N2" 
## [181] "N2"  "N1"  "N1"  "N0"  "N1"  "N2"  "N1"  "N1"  "N0"  "N0"  "N2"  "N1" 
## [193] "N1"  "N2"  "N0"  "N0"  "N2"  "N3b" "N2"  "N1"  "N3a" "N0"  "N1"  "N0" 
## [205] "N1"  "NX"  "N0"  "N3"  "N0"  "N1"  "N0"  "N3a" "N0"  "N0"  "N1"  "N3b"
## [217] "N0"  "N3"  "N3a" "N0"  "N1"  "N1"  "N0"  "N1"  "N2"  "N1"  "N2"  "NX" 
## [229] "N2"  "N3a" "N1"  "N1"  "N1"  "N0"  "N0"  "N1"  "N0"  "N2"  "N2"  "N2" 
## [241] "N0"  "NX"  "N2"  "N1"  "N3a" "N1"  "N2"  "N1"  "N2"  "N3a" "N3a" "N2" 
## [253] "N0"  "N0"  "N0"  "N0"  "N2"  "N3"  "N3"  "NX"  "N2"  "N1"  "N0"  "N1" 
## [265] "N2"  "N2"  "N1"  "N0"  "N1"  "N0"  "N0"  "N0"  "N2"  "N1"  "N0"  "N0" 
## [277] "N1"  "N0"  "N0"  "N1"  "N2"  "N3"  "N0"  "N1"  "NX"  "N0"  "N1"  "N3a"
## [289] "N3"  "N3a" "N1"  "N2"  "N1"  "N1"  "N1"  "N0"  "NX"  "N1"  "N1"  "N1" 
## [301] "N2"  "N0"  "N0"  "N3a" "N1"  "N0"  "N2"  "N1"  "N0"  "N2"  "N3a" "NX" 
## [313] "N0"  "N1"  "N0"  "N0"  "N1"  "N2"  "N2"  "N0"  "N2"  "N2"  "N3a" "N0" 
## [325] "N3a" "N2"  "N1"  "N1"  "N2"  "N0"  "N0"  "N0"  "N1"  "N3a" "N1"  "N1" 
## [337] "N3"  "N1"  "N0"  "N1"  "N0"  "N1"  "N3a" "N0"  "N1"  "N1"  "N2"  "N0" 
## [349] "N0"  "N2"  "N3"  "N1"  "N2"  "N3a" "NX"  "N1"  "N3"  "N0"  "N2"  "N3b"
## [361] "N0"  "N3a" "N3a" "N0"  "N1"  "N3a" "N0"  "N1"  "N1"  "N0"  "N0"  "N0" 
## [373] "N0"  "N1"  "N1"  "N0"  "N3"  "N0"  "N2"  "N0"  "N0"  "N2"  "N0"  "N2" 
## [385] "N3"  "N0"  "N0"  "N1"  "N1"  "N2"  "N3"  "N2"  "N2"  "N3a" "N0"  "NX" 
## [397] "N0"  "N0"  "N0"  "N0"  "N1"  "N2"  "N2"  "N3"  "N0"  "N3a" "N1"  "N0" 
## [409] "N1"  "N1"  "N1"  "N0"  "N3a" "N1"  "N1"
rse$ajcc_pathologic_m
##   [1] "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
##  [16] "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
##  [31] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "MX" "M0" "M0" "M0" "M0" "M0" "M0"
##  [46] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
##  [61] "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0"
##  [76] "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "MX" "M0" "M0" "MX" "M0" "M0"
##  [91] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [106] "M0" "M0" "M0" "MX" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1"
## [121] "M0" "MX" "M0" "M0" "M1" "M0" "MX" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [136] "M0" "M0" "MX" "M0" "M0" "M0" "MX" "M0" "M0" "M0" "M0" "MX" "M0" "M0" "M0"
## [151] "M0" "M0" "M0" "MX" "M1" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0"
## [166] "M1" "M0" "MX" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [181] "M1" "MX" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "MX"
## [196] "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "MX" "M0"
## [211] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [226] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [241] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "MX"
## [256] "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M1" "M0" "M0" "M0"
## [271] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0"
## [286] "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [301] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "MX" "M1"
## [316] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [331] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [346] "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0" "M0" "M0" "M1" "M0" "M0" "M0"
## [361] "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [376] "M0" "M0" "M0" "MX" "M0" "M0" "M0" "MX" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [391] "M0" "M0" "M0" "M0" "MX" "MX" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M0"
## [406] "MX" "M0" "M0" "M0" "M0" "M0" "M0" "M0" "M1" "M0"
rse$site_of_resection_or_biopsy
##   [1] "Fundus of stomach"                "Body of stomach"                 
##   [3] "Gastric antrum"                   "Gastric antrum"                  
##   [5] "Gastric antrum"                   "Body of stomach"                 
##   [7] "Body of stomach"                  "Body of stomach"                 
##   [9] "Body of stomach"                  "Cardia, NOS"                     
##  [11] "Gastric antrum"                   "Gastric antrum"                  
##  [13] "Gastric antrum"                   "Gastric antrum"                  
##  [15] "Body of stomach"                  "Gastric antrum"                  
##  [17] "Gastric antrum"                   "Body of stomach"                 
##  [19] "Body of stomach"                  "Body of stomach"                 
##  [21] "Fundus of stomach"                "Gastric antrum"                  
##  [23] "Gastric antrum"                   "Fundus of stomach"               
##  [25] "Stomach, NOS"                     "Body of stomach"                 
##  [27] "Body of stomach"                  "Gastric antrum"                  
##  [29] "Body of stomach"                  "Gastric antrum"                  
##  [31] "Stomach, NOS"                     "Cardia, NOS"                     
##  [33] "Fundus of stomach"                "Fundus of stomach"               
##  [35] "Body of stomach"                  "Cardia, NOS"                     
##  [37] "Gastric antrum"                   "Cardia, NOS"                     
##  [39] "Cardia, NOS"                      "Fundus of stomach"               
##  [41] "Cardia, NOS"                      "Fundus of stomach"               
##  [43] "Body of stomach"                  "Fundus of stomach"               
##  [45] "Cardia, NOS"                      "Gastric antrum"                  
##  [47] "Gastric antrum"                   "Cardia, NOS"                     
##  [49] "Body of stomach"                  "Cardia, NOS"                     
##  [51] "Fundus of stomach"                "Gastric antrum"                  
##  [53] "Cardia, NOS"                      "Gastric antrum"                  
##  [55] "Cardia, NOS"                      "Body of stomach"                 
##  [57] "Cardia, NOS"                      "Gastric antrum"                  
##  [59] "Body of stomach"                  "Gastric antrum"                  
##  [61] "Stomach, NOS"                     "Cardia, NOS"                     
##  [63] "Gastric antrum"                   "Gastric antrum"                  
##  [65] "Cardia, NOS"                      "Fundus of stomach"               
##  [67] "Fundus of stomach"                "Gastric antrum"                  
##  [69] "Gastric antrum"                   "Cardia, NOS"                     
##  [71] "Gastric antrum"                   "Gastric antrum"                  
##  [73] "Body of stomach"                  "Cardia, NOS"                     
##  [75] "Cardia, NOS"                      "Gastric antrum"                  
##  [77] "Body of stomach"                  "Cardia, NOS"                     
##  [79] "Cardia, NOS"                      "Fundus of stomach"               
##  [81] "Fundus of stomach"                "Fundus of stomach"               
##  [83] "Body of stomach"                  "Gastric antrum"                  
##  [85] "Body of stomach"                  "Gastric antrum"                  
##  [87] "Gastric antrum"                   "Cardia, NOS"                     
##  [89] "Gastric antrum"                   "Gastric antrum"                  
##  [91] "Gastric antrum"                   "Gastric antrum"                  
##  [93] "Body of stomach"                  "Body of stomach"                 
##  [95] "Gastric antrum"                   "Cardia, NOS"                     
##  [97] "Body of stomach"                  "Body of stomach"                 
##  [99] "Gastric antrum"                   "Body of stomach"                 
## [101] "Cardia, NOS"                      "Gastric antrum"                  
## [103] "Cardia, NOS"                      "Gastric antrum"                  
## [105] "Fundus of stomach"                "Cardia, NOS"                     
## [107] "Gastric antrum"                   "Gastric antrum"                  
## [109] "Body of stomach"                  "Fundus of stomach"               
## [111] "Body of stomach"                  "Body of stomach"                 
## [113] "Gastric antrum"                   "Body of stomach"                 
## [115] "Cardia, NOS"                      "Gastric antrum"                  
## [117] "Body of stomach"                  "Body of stomach"                 
## [119] "Cardia, NOS"                      "Gastric antrum"                  
## [121] "Stomach, NOS"                     "Body of stomach"                 
## [123] "Gastric antrum"                   "Gastric antrum"                  
## [125] "Body of stomach"                  "Body of stomach"                 
## [127] "Body of stomach"                  "Body of stomach"                 
## [129] "Body of stomach"                  "Stomach, NOS"                    
## [131] "Stomach, NOS"                     "Gastric antrum"                  
## [133] "Gastric antrum"                   "Stomach, NOS"                    
## [135] "Fundus of stomach"                "Body of stomach"                 
## [137] "Stomach, NOS"                     "Body of stomach"                 
## [139] "Body of stomach"                  "Fundus of stomach"               
## [141] "Gastric antrum"                   "Gastric antrum"                  
## [143] "Gastric antrum"                   "Gastric antrum"                  
## [145] "Gastric antrum"                   "Cardia, NOS"                     
## [147] "Body of stomach"                  "Body of stomach"                 
## [149] "Body of stomach"                  "Gastric antrum"                  
## [151] "Cardia, NOS"                      "Cardia, NOS"                     
## [153] "Body of stomach"                  "Cardia, NOS"                     
## [155] "Gastric antrum"                   "Cardia, NOS"                     
## [157] "Body of stomach"                  "Cardia, NOS"                     
## [159] "Cardia, NOS"                      "Cardia, NOS"                     
## [161] "Gastric antrum"                   "Gastric antrum"                  
## [163] "Gastric antrum"                   "Body of stomach"                 
## [165] "Gastric antrum"                   "Body of stomach"                 
## [167] "Fundus of stomach"                "Gastric antrum"                  
## [169] "Cardia, NOS"                      "Stomach, NOS"                    
## [171] "Cardia, NOS"                      "Body of stomach"                 
## [173] "Gastric antrum"                   "Gastric antrum"                  
## [175] "Cardia, NOS"                      "Gastric antrum"                  
## [177] "Gastric antrum"                   "Cardia, NOS"                     
## [179] "Body of stomach"                  "Gastric antrum"                  
## [181] "Gastric antrum"                   "Gastric antrum"                  
## [183] "Cardia, NOS"                      "Fundus of stomach"               
## [185] "Fundus of stomach"                "Body of stomach"                 
## [187] "Gastric antrum"                   "Body of stomach"                 
## [189] "Gastric antrum"                   "Gastric antrum"                  
## [191] "Body of stomach"                  "Gastric antrum"                  
## [193] "Cardia, NOS"                      "Fundus of stomach"               
## [195] "Cardia, NOS"                      "Cardia, NOS"                     
## [197] "Cardia, NOS"                      "Body of stomach"                 
## [199] "Gastric antrum"                   "Gastric antrum"                  
## [201] "Body of stomach"                  "Fundus of stomach"               
## [203] "Gastric antrum"                   "Fundus of stomach"               
## [205] "Gastric antrum"                   "Body of stomach"                 
## [207] "Gastric antrum"                   "Gastric antrum"                  
## [209] "Lesser curvature of stomach, NOS" "Body of stomach"                 
## [211] "Gastric antrum"                   "Cardia, NOS"                     
## [213] "Gastric antrum"                   "Body of stomach"                 
## [215] "Body of stomach"                  "Body of stomach"                 
## [217] "Gastric antrum"                   "Stomach, NOS"                    
## [219] "Gastric antrum"                   "Cardia, NOS"                     
## [221] "Cardia, NOS"                      "Stomach, NOS"                    
## [223] "Cardia, NOS"                      "Fundus of stomach"               
## [225] "Cardia, NOS"                      "Cardia, NOS"                     
## [227] "Cardia, NOS"                      "Fundus of stomach"               
## [229] "Cardia, NOS"                      "Fundus of stomach"               
## [231] "Gastric antrum"                   "Fundus of stomach"               
## [233] "Body of stomach"                  "Fundus of stomach"               
## [235] "Body of stomach"                  "Body of stomach"                 
## [237] "Cardia, NOS"                      "Cardia, NOS"                     
## [239] "Gastric antrum"                   "Cardia, NOS"                     
## [241] "Gastric antrum"                   "Cardia, NOS"                     
## [243] "Gastric antrum"                   "Gastric antrum"                  
## [245] "Fundus of stomach"                "Gastric antrum"                  
## [247] "Body of stomach"                  "Gastric antrum"                  
## [249] "Gastric antrum"                   "Cardia, NOS"                     
## [251] "Fundus of stomach"                "Body of stomach"                 
## [253] "Fundus of stomach"                "Cardia, NOS"                     
## [255] "Cardia, NOS"                      "Gastric antrum"                  
## [257] "Gastric antrum"                   "Stomach, NOS"                    
## [259] "Cardia, NOS"                      "Gastric antrum"                  
## [261] "Gastric antrum"                   "Gastric antrum"                  
## [263] "Body of stomach"                  "Gastric antrum"                  
## [265] "Fundus of stomach"                "Gastric antrum"                  
## [267] "Cardia, NOS"                      "Gastric antrum"                  
## [269] "Cardia, NOS"                      "Cardia, NOS"                     
## [271] "Gastric antrum"                   "Stomach, NOS"                    
## [273] "Gastric antrum"                   "Fundus of stomach"               
## [275] "Body of stomach"                  "Body of stomach"                 
## [277] "Body of stomach"                  "Gastric antrum"                  
## [279] "Body of stomach"                  "Gastric antrum"                  
## [281] "Cardia, NOS"                      "Body of stomach"                 
## [283] "Gastric antrum"                   "Pylorus"                         
## [285] "Fundus of stomach"                "Cardia, NOS"                     
## [287] "Body of stomach"                  "Gastric antrum"                  
## [289] "Gastric antrum"                   "Gastric antrum"                  
## [291] "Gastric antrum"                   "Cardia, NOS"                     
## [293] "Cardia, NOS"                      "Cardia, NOS"                     
## [295] "Gastric antrum"                   "Body of stomach"                 
## [297] "Body of stomach"                  "Cardia, NOS"                     
## [299] "Gastric antrum"                   "Gastric antrum"                  
## [301] "Cardia, NOS"                      "Gastric antrum"                  
## [303] "Cardia, NOS"                      "Gastric antrum"                  
## [305] "Body of stomach"                  "Stomach, NOS"                    
## [307] "Cardia, NOS"                      "Gastric antrum"                  
## [309] "Body of stomach"                  "Gastric antrum"                  
## [311] "Gastric antrum"                   "Gastric antrum"                  
## [313] "Gastric antrum"                   "Gastric antrum"                  
## [315] "Body of stomach"                  "Body of stomach"                 
## [317] "Body of stomach"                  "Gastric antrum"                  
## [319] "Cardia, NOS"                      "Fundus of stomach"               
## [321] "Body of stomach"                  "Gastric antrum"                  
## [323] "Gastric antrum"                   "Gastric antrum"                  
## [325] "Gastric antrum"                   "Gastric antrum"                  
## [327] "Cardia, NOS"                      "Body of stomach"                 
## [329] "Gastric antrum"                   "Cardia, NOS"                     
## [331] "Gastric antrum"                   "Gastric antrum"                  
## [333] "Stomach, NOS"                     "Body of stomach"                 
## [335] "Gastric antrum"                   "Cardia, NOS"                     
## [337] "Fundus of stomach"                "Body of stomach"                 
## [339] "Body of stomach"                  "Gastric antrum"                  
## [341] "Gastric antrum"                   "Gastric antrum"                  
## [343] "Fundus of stomach"                "Cardia, NOS"                     
## [345] "Fundus of stomach"                "Cardia, NOS"                     
## [347] "Gastric antrum"                   "Body of stomach"                 
## [349] "Cardia, NOS"                      "Cardia, NOS"                     
## [351] "Gastric antrum"                   "Gastric antrum"                  
## [353] "Fundus of stomach"                "Body of stomach"                 
## [355] "Gastric antrum"                   "Gastric antrum"                  
## [357] "Cardia, NOS"                      "Cardia, NOS"                     
## [359] "Cardia, NOS"                      "Gastric antrum"                  
## [361] "Cardia, NOS"                      "Cardia, NOS"                     
## [363] "Cardia, NOS"                      "Gastric antrum"                  
## [365] "Cardia, NOS"                      "Cardia, NOS"                     
## [367] "Gastric antrum"                   "Fundus of stomach"               
## [369] "Body of stomach"                  "Cardia, NOS"                     
## [371] "Body of stomach"                  "Cardia, NOS"                     
## [373] "Cardia, NOS"                      "Fundus of stomach"               
## [375] "Gastric antrum"                   "Body of stomach"                 
## [377] "Fundus of stomach"                "Fundus of stomach"               
## [379] "Stomach, NOS"                     "Gastric antrum"                  
## [381] "Fundus of stomach"                "Gastric antrum"                  
## [383] "Stomach, NOS"                     "Gastric antrum"                  
## [385] "Cardia, NOS"                      "Gastric antrum"                  
## [387] "Body of stomach"                  "Cardia, NOS"                     
## [389] "Gastric antrum"                   "Cardia, NOS"                     
## [391] "Cardia, NOS"                      "Gastric antrum"                  
## [393] "Body of stomach"                  "Body of stomach"                 
## [395] "Gastric antrum"                   "Stomach, NOS"                    
## [397] "Gastric antrum"                   "Body of stomach"                 
## [399] "Body of stomach"                  "Fundus of stomach"               
## [401] "Gastric antrum"                   "Body of stomach"                 
## [403] "Body of stomach"                  "Body of stomach"                 
## [405] "Cardia, NOS"                      "Gastric antrum"                  
## [407] "Gastric antrum"                   "Body of stomach"                 
## [409] "Cardia, NOS"                      "Gastric antrum"                  
## [411] "Gastric antrum"                   "Fundus of stomach"               
## [413] "Cardia, NOS"                      "Cardia, NOS"                     
## [415] "Fundus of stomach"
rse$gender
##   [1] "male"   "female" "male"   "female" "female" "female" "female" "male"  
##   [9] "male"   "female" "male"   "female" "male"   "male"   "female" "male"  
##  [17] "female" "female" "female" "male"   "female" "male"   "male"   "female"
##  [25] "female" "male"   "male"   "male"   "male"   "female" "male"   "male"  
##  [33] "male"   "female" "male"   "male"   "male"   "male"   "male"   "male"  
##  [41] "male"   "male"   "male"   "female" "male"   "female" "male"   "male"  
##  [49] "male"   "male"   "male"   "female" "male"   "male"   "female" "female"
##  [57] "male"   "female" "female" "male"   "male"   "male"   "male"   "male"  
##  [65] "male"   "male"   "female" "male"   "male"   "male"   "male"   "female"
##  [73] "male"   "female" "male"   "male"   "male"   "female" "female" "male"  
##  [81] "male"   "female" "male"   "male"   "male"   "male"   "female" "male"  
##  [89] "female" "male"   "male"   "male"   "male"   "female" "female" "male"  
##  [97] "male"   "male"   "male"   "male"   "male"   "male"   "male"   "male"  
## [105] "male"   "male"   "male"   "male"   "female" "male"   "male"   "male"  
## [113] "male"   "male"   "male"   "female" "female" "male"   "male"   "male"  
## [121] "female" "male"   "male"   "male"   "female" "male"   "female" "female"
## [129] "male"   "female" "female" "male"   "female" "female" "female" "male"  
## [137] "male"   "male"   "male"   "male"   "male"   "female" "male"   "female"
## [145] "male"   "male"   "male"   "female" "female" "female" "male"   "male"  
## [153] "male"   "male"   "male"   "female" "male"   "female" "female" "male"  
## [161] "male"   "female" "female" "male"   "female" "male"   "male"   "female"
## [169] "female" "female" "male"   "female" "male"   "male"   "male"   "male"  
## [177] "female" "male"   "male"   "female" "male"   "male"   "male"   "male"  
## [185] "male"   "male"   "female" "female" "female" "male"   "male"   "female"
## [193] "male"   "female" "male"   "male"   "female" "male"   "male"   "female"
## [201] "male"   "male"   "female" "female" "male"   "female" "male"   "male"  
## [209] "male"   "female" "male"   "male"   "female" "female" "male"   "male"  
## [217] "male"   "male"   "female" "male"   "male"   "male"   "male"   "female"
## [225] "male"   "female" "male"   "male"   "male"   "male"   "male"   "male"  
## [233] "female" "male"   "male"   "male"   "male"   "male"   "male"   "male"  
## [241] "female" "male"   "male"   "male"   "male"   "male"   "male"   "male"  
## [249] "female" "male"   "female" "male"   "female" "female" "male"   "female"
## [257] "male"   "female" "male"   "male"   "male"   "male"   "male"   "male"  
## [265] "female" "male"   "male"   "female" "female" "female" "female" "male"  
## [273] "male"   "female" "female" "male"   "female" "female" "female" "female"
## [281] "female" "female" "male"   "male"   "male"   "male"   "male"   "female"
## [289] "male"   "female" "female" "male"   "male"   "female" "female" "male"  
## [297] "male"   "male"   "male"   "male"   "male"   "male"   "male"   "male"  
## [305] "male"   "male"   "female" "male"   "female" "female" "female" "female"
## [313] "male"   "male"   "female" "male"   "female" "male"   "female" "female"
## [321] "male"   "male"   "female" "male"   "female" "female" "male"   "female"
## [329] "male"   "male"   "male"   "male"   "male"   "female" "female" "male"  
## [337] "male"   "female" "male"   "female" "male"   "male"   "male"   "male"  
## [345] "male"   "female" "female" "female" "male"   "male"   "male"   "male"  
## [353] "male"   "female" "female" "male"   "male"   "male"   "female" "female"
## [361] "male"   "male"   "male"   "male"   "male"   "female" "male"   "male"  
## [369] "male"   "female" "male"   "male"   "female" "female" "male"   "female"
## [377] "male"   "male"   "male"   "male"   "female" "male"   "female" "female"
## [385] "female" "female" "female" "male"   "female" "male"   "male"   "female"
## [393] "female" "male"   "male"   "male"   "male"   "male"   "male"   "male"  
## [401] "male"   "female" "female" "male"   "female" "male"   "male"   "male"  
## [409] "male"   "male"   "male"   "female" "male"   "female" "male"
rse$paper_Lauren.Class
##   [1] Mixed      Intestinal Intestinal Intestinal Diffuse    Diffuse   
##   [7] Diffuse    Intestinal <NA>       <NA>       Intestinal <NA>      
##  [13] Intestinal Intestinal <NA>       Diffuse    Intestinal Intestinal
##  [19] Intestinal <NA>       <NA>       Diffuse    <NA>       <NA>      
##  [25] NA         Intestinal Intestinal <NA>       <NA>       <NA>      
##  [31] Intestinal Mixed      <NA>       Intestinal Intestinal Diffuse   
##  [37] Diffuse    Intestinal Intestinal Intestinal <NA>       Intestinal
##  [43] Intestinal <NA>       Intestinal <NA>       Intestinal Diffuse   
##  [49] Intestinal <NA>       Intestinal Intestinal Diffuse    Diffuse   
##  [55] NA         <NA>       Mixed      <NA>       Intestinal <NA>      
##  [61] <NA>       Diffuse    Intestinal Intestinal <NA>       Mixed     
##  [67] Intestinal Intestinal Intestinal Intestinal <NA>       Diffuse   
##  [73] Intestinal Intestinal Intestinal Intestinal Intestinal <NA>      
##  [79] Intestinal <NA>       Mixed      Diffuse    <NA>       Diffuse   
##  [85] <NA>       Diffuse    <NA>       Intestinal Intestinal Intestinal
##  [91] Intestinal Intestinal Intestinal <NA>       Intestinal Intestinal
##  [97] Diffuse    Intestinal Diffuse    Intestinal Intestinal <NA>      
## [103] <NA>       Intestinal <NA>       Intestinal Diffuse    Intestinal
## [109] Mixed      <NA>       Intestinal Diffuse    Diffuse    <NA>      
## [115] Intestinal Intestinal Intestinal Intestinal Intestinal Diffuse   
## [121] Intestinal Intestinal <NA>       <NA>       Diffuse    Diffuse   
## [127] NA         Intestinal <NA>       Diffuse    Diffuse    Mixed     
## [133] <NA>       Intestinal Intestinal Diffuse    Intestinal <NA>      
## [139] Intestinal Intestinal Intestinal Intestinal Intestinal Diffuse   
## [145] Intestinal <NA>       NA         Intestinal Intestinal Mixed     
## [151] <NA>       <NA>       Intestinal Intestinal Intestinal Intestinal
## [157] <NA>       Intestinal Intestinal <NA>       <NA>       Intestinal
## [163] <NA>       <NA>       Diffuse    <NA>       Intestinal <NA>      
## [169] Mixed      <NA>       <NA>       Diffuse    Diffuse    <NA>      
## [175] Intestinal Diffuse    Intestinal <NA>       <NA>       Intestinal
## [181] <NA>       Intestinal <NA>       Intestinal NA         Diffuse   
## [187] <NA>       <NA>       Intestinal <NA>       <NA>       <NA>      
## [193] Mixed      NA         Mixed      Intestinal <NA>       <NA>      
## [199] <NA>       Diffuse    Intestinal Intestinal <NA>       Diffuse   
## [205] Diffuse    <NA>       Intestinal <NA>       <NA>       <NA>      
## [211] Intestinal <NA>       <NA>       Diffuse    Intestinal Intestinal
## [217] Diffuse    Intestinal <NA>       <NA>       Intestinal Intestinal
## [223] Diffuse    Diffuse    Diffuse    Intestinal <NA>       <NA>      
## [229] <NA>       Intestinal Intestinal Intestinal <NA>       Intestinal
## [235] Diffuse    <NA>       Intestinal Diffuse    Intestinal Mixed     
## [241] Diffuse    Intestinal <NA>       Intestinal Intestinal Intestinal
## [247] <NA>       Diffuse    Diffuse    <NA>       Mixed      <NA>      
## [253] Mixed      Intestinal Intestinal Intestinal Intestinal Diffuse   
## [259] <NA>       Diffuse    Intestinal Intestinal Intestinal <NA>      
## [265] Diffuse    Intestinal <NA>       Diffuse    <NA>       <NA>      
## [271] <NA>       <NA>       <NA>       Intestinal Intestinal <NA>      
## [277] Intestinal NA         <NA>       <NA>       <NA>       NA        
## [283] <NA>       Intestinal <NA>       <NA>       <NA>       <NA>      
## [289] <NA>       Mixed      Intestinal <NA>       <NA>       <NA>      
## [295] Diffuse    Intestinal Intestinal <NA>       Intestinal <NA>      
## [301] Intestinal <NA>       Intestinal Diffuse    <NA>       <NA>      
## [307] <NA>       Intestinal Intestinal Intestinal Diffuse    Intestinal
## [313] <NA>       Intestinal Intestinal Intestinal Intestinal <NA>      
## [319] Intestinal Diffuse    Intestinal Intestinal <NA>       Intestinal
## [325] Intestinal Diffuse    Intestinal Intestinal Intestinal <NA>      
## [331] Diffuse    <NA>       Diffuse    Diffuse    Intestinal Intestinal
## [337] <NA>       Intestinal Intestinal Intestinal Intestinal Intestinal
## [343] Mixed      Intestinal Intestinal <NA>       NA         Intestinal
## [349] <NA>       <NA>       Mixed      Diffuse    <NA>       Diffuse   
## [355] Intestinal Intestinal Diffuse    <NA>       <NA>       Intestinal
## [361] <NA>       Intestinal <NA>       Diffuse    <NA>       <NA>      
## [367] Intestinal NA         <NA>       Intestinal Intestinal <NA>      
## [373] Diffuse    Intestinal Intestinal Intestinal <NA>       Diffuse   
## [379] <NA>       <NA>       NA         Intestinal <NA>       Intestinal
## [385] <NA>       Intestinal Intestinal <NA>       Intestinal <NA>      
## [391] <NA>       Diffuse    Diffuse    <NA>       <NA>       <NA>      
## [397] Intestinal Intestinal Intestinal Intestinal Intestinal Intestinal
## [403] Intestinal Intestinal Intestinal Mixed      Intestinal Intestinal
## [409] Diffuse    Mixed      Intestinal Intestinal Intestinal <NA>      
## [415] Intestinal
## Levels: Diffuse Intestinal Mixed NA
rse$paper_Age.at.Initial.Diagnosis
##   [1] 74.82 58.62 54.93 53.84 53.82 67    56.92 59.86 <NA>  <NA>  75.42 <NA> 
##  [13] 59.19 81.33 <NA>  78.9  75.56 70.8  71.98 <NA>  <NA>  82.99 <NA>  <NA> 
##  [25] 66.42 60.79 62.4  <NA>  <NA>  <NA>  76.84 63.12 <NA>  63.2  67.06 75.55
##  [37] 53.47 59.49 74.24 73.32 <NA>  65.15 75.55 <NA>  57.06 <NA>  58.35 83.17
##  [49] 64.3  <NA>  72.48 76.8  64.64 55.19 64.25 <NA>  62.15 <NA>  73.02 <NA> 
##  [61] <NA>  62.65 45.55 87.68 <NA>  62.8  70.28 49.58 69.26 62.4  <NA>  69.09
##  [73] 69.83 54.36 68.12 49.1  80.46 <NA>  69.21 <NA>  75.87 66.95 <NA>  69.22
##  [85] <NA>  39.58 <NA>  68.17 82.62 77.46 49.19 70.76 76.69 <NA>  51    66.74
##  [97] 60.22 65.48 47.95 59.79 79.63 <NA>  <NA>  79.97 <NA>  52.8  58.77 72.31
## [109] 71.91 <NA>  51.2  72.05 70.89 <NA>  63.25 72.56 67.02 83.58 50.39 51.98
## [121] 78.07 58.3  <NA>  <NA>  50.7  54.93 60.77 78.93 <NA>  76.37 74.41 70.03
## [133] <NA>  NA    72.1  58.11 57.33 <NA>  70.61 71.82 61.02 71.97 79.55 76.97
## [145] 73.92 <NA>  77.49 62.5  71.45 54.8  <NA>  <NA>  53.09 62.83 65.65 53.85
## [157] <NA>  66.68 75.34 <NA>  <NA>  70.99 <NA>  <NA>  43.77 <NA>  57.14 <NA> 
## [169] 71.31 <NA>  <NA>  51.19 60.06 <NA>  74.01 48.08 58.92 <NA>  <NA>  72.4 
## [181] <NA>  90    <NA>  55.16 56.75 65.1  <NA>  <NA>  86.75 <NA>  <NA>  <NA> 
## [193] 80.06 71.18 79.75 74.49 <NA>  <NA>  <NA>  69.6  57.08 76.76 <NA>  70.43
## [205] 69.47 <NA>  69.67 <NA>  <NA>  <NA>  49.75 <NA>  <NA>  54.07 68.66 66.22
## [217] 41.69 70.08 <NA>  <NA>  NA    72.72 71.66 63.34 65.7  64.1  <NA>  <NA> 
## [229] <NA>  77.24 58.16 61.83 <NA>  57.39 69.53 <NA>  84.92 68.92 71.73 68.53
## [241] 61.45 75.31 <NA>  62.21 63.92 61.02 <NA>  61.74 67.59 <NA>  68.02 <NA> 
## [253] 80.48 58.66 77.25 64.07 56.33 72.58 <NA>  56.49 73.1  69    81.34 <NA> 
## [265] 42.13 90    <NA>  78.33 <NA>  <NA>  <NA>  <NA>  <NA>  73.49 60.93 <NA> 
## [277] 80.49 73.86 <NA>  <NA>  <NA>  68.92 <NA>  90    <NA>  <NA>  <NA>  <NA> 
## [289] <NA>  72.62 82.15 <NA>  <NA>  <NA>  34.5  74.17 65.05 <NA>  56.67 <NA> 
## [301] 58.11 <NA>  76.71 72.79 <NA>  <NA>  <NA>  57.79 64.08 66.04 74.53 79.43
## [313] <NA>  70.9  54.66 65.33 78.75 <NA>  67    55.24 76.42 53.3  <NA>  52.47
## [325] 67.73 45.71 83.42 57.68 59.5  <NA>  55.01 <NA>  43.98 68.65 79.95 69.91
## [337] <NA>  74.71 70.19 71.88 72.88 45.97 55.97 58.87 63.65 <NA>  78.77 67.77
## [349] <NA>  <NA>  59.58 45.27 <NA>  72.68 74.87 73.99 59.05 <NA>  <NA>  58.85
## [361] <NA>  56.79 <NA>  58.91 <NA>  <NA>  69.06 51.59 <NA>  68.41 75.22 <NA> 
## [373] 53.13 65.01 NA    69.34 <NA>  52    <NA>  <NA>  84.53 74.65 <NA>  70.95
## [385] <NA>  71.82 70.68 <NA>  62.18 <NA>  <NA>  60.58 46.9  <NA>  <NA>  <NA> 
## [397] 85.83 77.25 75.37 60.05 80.6  58.94 70.67 63.36 81.42 78    63.7  68.42
## [409] 58.75 51.18 56.71 90    44.22 <NA>  59.03
## 278 Levels: 34.5 39.58 41.69 41.93 42.13 43.77 43.98 44.22 45.27 45.55 ... NA
rse$paper_ARID1A.mutation
##   [1] 1    0    1    1    0    0    1    1    <NA> <NA> 0    <NA> 0    0    <NA>
##  [16] NA   1    1    0    <NA> <NA> 0    <NA> <NA> 1    0    1    <NA> <NA> <NA>
##  [31] 0    0    <NA> 0    0    0    1    0    0    1    <NA> NA   0    <NA> 0   
##  [46] <NA> 0    1    0    <NA> 1    0    1    0    1    <NA> 1    <NA> 1    <NA>
##  [61] <NA> 0    1    0    <NA> 0    0    NA   1    0    <NA> 1    0    0    0   
##  [76] 0    0    <NA> 0    <NA> 0    0    <NA> 0    <NA> 0    <NA> 1    0    1   
##  [91] 0    0    0    <NA> 0    0    0    1    0    0    1    <NA> <NA> 0    <NA>
## [106] 0    0    0    1    <NA> 0    0    0    <NA> 0    0    0    0    0    1   
## [121] 0    0    <NA> <NA> 0    0    1    1    <NA> 0    1    0    <NA> 0    0   
## [136] 0    0    <NA> 1    0    0    0    1    0    1    <NA> 1    0    1    0   
## [151] <NA> <NA> 0    0    0    1    <NA> 1    0    <NA> <NA> 0    <NA> <NA> 0   
## [166] <NA> 0    <NA> 1    <NA> <NA> 1    0    <NA> 0    0    0    <NA> <NA> 0   
## [181] <NA> 1    <NA> 1    1    1    <NA> <NA> 0    <NA> <NA> <NA> 0    1    1   
## [196] 1    <NA> <NA> <NA> 1    0    0    <NA> 1    1    <NA> 0    <NA> <NA> <NA>
## [211] 0    <NA> <NA> 0    0    0    0    1    <NA> <NA> 0    0    0    0    0   
## [226] 0    <NA> <NA> <NA> 0    1    0    <NA> 0    0    <NA> 0    0    1    0   
## [241] 0    0    <NA> 0    1    1    <NA> 0    0    <NA> 0    <NA> 0    0    0   
## [256] 1    0    0    <NA> 0    0    0    0    <NA> 0    1    <NA> 1    <NA> <NA>
## [271] <NA> <NA> <NA> 0    0    <NA> 1    1    <NA> <NA> <NA> 0    <NA> 0    <NA>
## [286] <NA> <NA> <NA> <NA> 1    0    <NA> <NA> <NA> 0    1    0    <NA> 0    <NA>
## [301] 0    <NA> 1    0    <NA> <NA> <NA> 0    0    1    1    0    <NA> 0    0   
## [316] 0    0    <NA> 1    0    0    0    <NA> 0    1    0    1    0    0    <NA>
## [331] NA   <NA> 0    0    0    0    <NA> 1    0    1    0    0    0    0    1   
## [346] <NA> 1    1    <NA> <NA> 0    0    <NA> 0    1    1    0    <NA> <NA> 0   
## [361] <NA> 0    <NA> 0    <NA> <NA> 0    1    <NA> 1    1    <NA> 0    0    1   
## [376] 0    <NA> 0    <NA> <NA> 1    0    <NA> 1    <NA> 0    0    <NA> 0    <NA>
## [391] <NA> 0    0    <NA> <NA> <NA> 1    0    1    1    1    0    0    0    0   
## [406] 1    1    0    0    0    NA   0    0    <NA> 0   
## Levels: 0 1 NA
rse$paper_CDKN2A.Epigenetically.Silenced
##   [1] false false false false false true  true  true  <NA>  <NA>  false <NA> 
##  [13] NA    NA    <NA>  NA    NA    true  NA    <NA>  <NA>  false <NA>  <NA> 
##  [25] NA    true  true  <NA>  <NA>  <NA>  NA    true  <NA>  true  false false
##  [37] true  false false false <NA>  true  false <NA>  NA    <NA>  true  false
##  [49] false <NA>  false false true  true  true  <NA>  false <NA>  NA    <NA> 
##  [61] <NA>  false false NA    <NA>  false false NA    NA    false <NA>  NA   
##  [73] NA    NA    false false false <NA>  false <NA>  false true  <NA>  false
##  [85] <NA>  true  <NA>  false true  true  false true  NA    <NA>  false false
##  [97] false false false false false <NA>  <NA>  false <NA>  false false false
## [109] NA    <NA>  NA    true  false <NA>  true  NA    false false true  false
## [121] NA    NA    <NA>  <NA>  false false NA    true  <NA>  NA    NA    NA   
## [133] <NA>  false false false NA    <NA>  true  false true  false true  false
## [145] false <NA>  true  false true  false <NA>  <NA>  false false false true 
## [157] <NA>  NA    NA    <NA>  <NA>  true  <NA>  <NA>  false <NA>  false <NA> 
## [169] true  <NA>  <NA>  false false <NA>  false false true  <NA>  <NA>  false
## [181] <NA>  true  <NA>  true  true  false <NA>  <NA>  false <NA>  <NA>  <NA> 
## [193] true  true  false true  <NA>  <NA>  <NA>  true  false false <NA>  false
## [205] true  <NA>  false <NA>  <NA>  <NA>  false <NA>  <NA>  false false NA   
## [217] false NA    <NA>  <NA>  false NA    false false NA    false <NA>  <NA> 
## [229] <NA>  false false false <NA>  true  false <NA>  NA    false NA    NA   
## [241] false NA    <NA>  true  true  false <NA>  false NA    <NA>  false <NA> 
## [253] true  NA    false true  NA    NA    <NA>  NA    false true  true  <NA> 
## [265] false NA    <NA>  false <NA>  <NA>  <NA>  <NA>  <NA>  false NA    <NA> 
## [277] NA    true  <NA>  <NA>  <NA>  NA    <NA>  false <NA>  <NA>  <NA>  <NA> 
## [289] <NA>  false NA    <NA>  <NA>  <NA>  false false NA    <NA>  NA    <NA> 
## [301] true  <NA>  true  false <NA>  <NA>  <NA>  false false false false NA   
## [313] <NA>  false false false false <NA>  false false NA    false <NA>  true 
## [325] false false true  false false <NA>  false <NA>  NA    true  false true 
## [337] <NA>  false true  false false true  false false true  <NA>  NA    true 
## [349] <NA>  <NA>  false false <NA>  false NA    false false <NA>  <NA>  false
## [361] <NA>  false <NA>  false <NA>  <NA>  false true  <NA>  true  false <NA> 
## [373] false false true  true  <NA>  false <NA>  <NA>  false false <NA>  false
## [385] <NA>  true  false <NA>  false <NA>  <NA>  false false <NA>  <NA>  <NA> 
## [397] NA    false true  true  NA    NA    false false NA    true  false NA   
## [409] false false false false true  <NA>  false
## Levels: false NA true
rse$paper_Country
##   [1] Vietnam       Russia        Korea_South   Korea_South   Russia       
##   [6] Germany       Korea_South   Russia        <NA>          <NA>         
##  [11] Vietnam       <NA>          Ukraine       Germany       <NA>         
##  [16] Russia        Ukraine       Russia        Russia        <NA>         
##  [21] <NA>          Vietnam       <NA>          <NA>          Russia       
##  [26] Russia        Russia        <NA>          <NA>          <NA>         
##  [31] Germany       Ukraine       <NA>          Russia        Russia       
##  [36] Poland        Poland        Russia        United_States Poland       
##  [41] <NA>          Russia        Korea_South   <NA>          Vietnam      
##  [46] <NA>          Vietnam       Germany       Poland        <NA>         
##  [51] Russia        Ukraine       Ukraine       Ukraine       Ukraine      
##  [56] <NA>          Ukraine       <NA>          Russia        <NA>         
##  [61] <NA>          Ukraine       Vietnam       Russia        <NA>         
##  [66] Russia        Russia        Germany       Germany       Poland       
##  [71] <NA>          Germany       Germany       Ukraine       Vietnam      
##  [76] Vietnam       Poland        <NA>          Ukraine       <NA>         
##  [81] Poland        Vietnam       <NA>          Ukraine       <NA>         
##  [86] Vietnam       <NA>          United_States Korea_South   Korea_South  
##  [91] Russia        United_States Korea_South   <NA>          Vietnam      
##  [96] Germany       Vietnam       Russia        Vietnam       Ukraine      
## [101] United_States <NA>          <NA>          United_States <NA>         
## [106] Vietnam       Poland        Russia        United_States <NA>         
## [111] Russia        Korea_South   Vietnam       <NA>          Russia       
## [116] Vietnam       Poland        Germany       United_States Vietnam      
## [121] Russia        Russia        <NA>          <NA>          Russia       
## [126] Russia        Russia        Russia        <NA>          Russia       
## [131] Russia        Ukraine       <NA>          Canada        Russia       
## [136] Russia        Germany       <NA>          Korea_South   Korea_South  
## [141] Poland        United_States Russia        Korea_South   Germany      
## [146] <NA>          United_States Russia        Russia        Poland       
## [151] <NA>          <NA>          Poland        United_States Vietnam      
## [156] Poland        <NA>          Russia        Germany       <NA>         
## [161] <NA>          Ukraine       <NA>          <NA>          Vietnam      
## [166] <NA>          Poland        <NA>          Ukraine       <NA>         
## [171] <NA>          Russia        Russia        <NA>          Ukraine      
## [176] United_States Korea_South   <NA>          <NA>          Korea_South  
## [181] <NA>          United_States <NA>          United_States Russia       
## [186] Poland        <NA>          <NA>          Vietnam       <NA>         
## [191] <NA>          <NA>          United_States Russia        United_States
## [196] Korea_South   <NA>          <NA>          <NA>          Poland       
## [201] Russia        Russia        <NA>          Ukraine       Vietnam      
## [206] <NA>          Ukraine       <NA>          <NA>          <NA>         
## [211] United_States <NA>          <NA>          Russia        Germany      
## [216] Korea_South   Vietnam       Germany       <NA>          <NA>         
## [221] Canada        Russia        Germany       Russia        Ukraine      
## [226] Poland        <NA>          <NA>          <NA>          Russia       
## [231] Germany       Russia        <NA>          Poland        Ukraine      
## [236] <NA>          Germany       United_States Korea_South   United_States
## [241] Vietnam       Russia        <NA>          Vietnam       Russia       
## [246] Korea_South   <NA>          Russia        Germany       <NA>         
## [251] Russia        <NA>          Ukraine       Germany       United_States
## [256] Ukraine       Germany       Germany       <NA>          Russia       
## [261] Korea_South   Vietnam       Russia        <NA>          Russia       
## [266] Germany       <NA>          Vietnam       <NA>          <NA>         
## [271] <NA>          <NA>          <NA>          Vietnam       Russia       
## [276] <NA>          Russia        Russia        <NA>          <NA>         
## [281] <NA>          Germany       <NA>          Vietnam       <NA>         
## [286] <NA>          <NA>          <NA>          <NA>          Russia       
## [291] Vietnam       <NA>          <NA>          <NA>          Vietnam      
## [296] Russia        Russia        <NA>          Korea_South   <NA>         
## [301] Poland        <NA>          Vietnam       Poland        <NA>         
## [306] <NA>          <NA>          Vietnam       Russia        Poland       
## [311] Ukraine       Russia        <NA>          United_States Germany      
## [316] Russia        Germany       <NA>          Russia        Russia       
## [321] Germany       Poland        <NA>          Vietnam       Ukraine      
## [326] Vietnam       Germany       Ukraine       Ukraine       <NA>         
## [331] Ukraine       <NA>          Russia        Ukraine       Vietnam      
## [336] United_States <NA>          Russia        Russia        Korea_South  
## [341] Poland        Korea_South   Ukraine       Russia        Poland       
## [346] <NA>          Russia        Korea_South   <NA>          <NA>         
## [351] Germany       Vietnam       <NA>          Russia        Russia       
## [356] Korea_South   United_States <NA>          <NA>          Korea_South  
## [361] <NA>          Poland        <NA>          Vietnam       <NA>         
## [366] <NA>          Korea_South   Ukraine       <NA>          Russia       
## [371] Korea_South   <NA>          Ukraine       Ukraine       Canada       
## [376] Russia        <NA>          Vietnam       <NA>          <NA>         
## [381] Ukraine       Korea_South   <NA>          Korea_South   <NA>         
## [386] Korea_South   Poland        <NA>          Korea_South   <NA>         
## [391] <NA>          Poland        Russia        <NA>          <NA>         
## [396] <NA>          Germany       Poland        Ukraine       Vietnam      
## [401] Russia        Russia        Poland        Poland        Germany      
## [406] United_States Vietnam       Germany       Germany       Vietnam      
## [411] Vietnam       Russia        Poland        <NA>          Vietnam      
## 8 Levels: Canada Germany Korea_South Poland Russia Ukraine ... Vietnam
rse$paper_Days.to.Death
##   [1] NA   NA   NA   NA   NA   NA   NA   422  <NA> <NA> 292  <NA> NA   NA   <NA>
##  [16] NA   NA   NA   NA   <NA> <NA> NA   <NA> <NA> NA   NA   NA   <NA> <NA> <NA>
##  [31] NA   518  <NA> NA   279  NA   NA   NA   NA   NA   <NA> NA   NA   <NA> NA  
##  [46] <NA> NA   NA   NA   <NA> 439  NA   NA   NA   NA   <NA> 466  <NA> NA   <NA>
##  [61] <NA> 350  NA   NA   <NA> NA   NA   NA   NA   312  <NA> 273  NA   NA   NA  
##  [76] NA   NA   <NA> NA   <NA> NA   NA   <NA> NA   <NA> NA   <NA> NA   NA   NA  
##  [91] NA   NA   NA   <NA> NA   2100 NA   NA   NA   NA   NA   <NA> <NA> 2197 <NA>
## [106] NA   NA   NA   777  <NA> 187  NA   NA   <NA> NA   NA   NA   426  NA   98  
## [121] 201  NA   <NA> <NA> NA   NA   NA   NA   <NA> NA   NA   NA   <NA> NA   NA  
## [136] NA   NA   <NA> NA   NA   NA   243  NA   NA   850  <NA> NA   NA   NA   445 
## [151] <NA> <NA> NA   NA   NA   NA   <NA> 940  NA   <NA> <NA> NA   <NA> <NA> NA  
## [166] <NA> NA   <NA> NA   <NA> <NA> NA   NA   <NA> 82   153  NA   <NA> <NA> NA  
## [181] <NA> NA   <NA> NA   NA   NA   <NA> <NA> NA   <NA> <NA> <NA> NA   NA   NA  
## [196] NA   <NA> <NA> <NA> NA   81   NA   <NA> 448  NA   <NA> NA   <NA> <NA> <NA>
## [211] 1796 <NA> <NA> NA   243  180  NA   215  <NA> <NA> NA   NA   0    NA   NA  
## [226] NA   <NA> <NA> <NA> NA   NA   NA   <NA> NA   NA   <NA> NA   20   3    128 
## [241] NA   NA   <NA> NA   NA   NA   <NA> NA   NA   <NA> NA   <NA> NA   NA   99  
## [256] NA   NA   0    <NA> 141  NA   386  NA   <NA> NA   31   <NA> NA   <NA> <NA>
## [271] <NA> <NA> <NA> NA   NA   <NA> NA   NA   <NA> <NA> <NA> 122  <NA> NA   <NA>
## [286] <NA> <NA> <NA> <NA> 245  NA   <NA> <NA> <NA> NA   NA   NA   <NA> NA   <NA>
## [301] 406  <NA> NA   NA   <NA> <NA> <NA> NA   NA   NA   NA   NA   <NA> NA   NA  
## [316] NA   1095 <NA> NA   NA   NA   NA   <NA> NA   NA   NA   NA   558  NA   <NA>
## [331] NA   <NA> 291  741  NA   NA   <NA> 525  NA   NA   NA   NA   NA   NA   NA  
## [346] <NA> NA   NA   <NA> <NA> 335  NA   <NA> 291  NA   NA   105  <NA> <NA> NA  
## [361] <NA> NA   <NA> NA   <NA> <NA> NA   NA   <NA> NA   NA   <NA> NA   NA   NA  
## [376] NA   <NA> NA   <NA> <NA> NA   NA   <NA> NA   <NA> NA   NA   <NA> NA   <NA>
## [391] <NA> NA   NA   <NA> <NA> <NA> NA   NA   NA   NA   NA   NA   NA   NA   NA  
## [406] 335  5    NA   211  NA   NA   NA   NA   <NA> NA  
## 52 Levels: 0 10 105 1095 122 128 141 153 16 1796 180 187 20 201 2100 ... NA
rse$paper_Days.to.Last.Follow.up
##   [1] 0    21   170  544  537  0    595  399  <NA> <NA> 10   <NA> 202  580  <NA>
##  [16] 0    0    373  0    <NA> <NA> 61   <NA> <NA> 0    388  356  <NA> <NA> <NA>
##  [31] 699  372  <NA> 5    19   582  543  569  76   508  <NA> 11   23   <NA> 0   
##  [46] <NA> 386  3196 353  <NA> 25   407  3    7    423  <NA> 5    <NA> 0    <NA>
##  [61] <NA> 3    468  0    <NA> 65   51   365  485  312  <NA> NA   0    308  0   
##  [76] 6    385  <NA> 0    <NA> 6    0    <NA> 99   <NA> 6    <NA> 17   368  270 
##  [91] 394  591  431  <NA> 406  1674 0    23   389  432  412  <NA> <NA> NA   <NA>
## [106] 0    566  22   NA   <NA> 0    64   413  <NA> 21   0    523  NA   645  5   
## [121] 0    0    <NA> <NA> 21   484  0    257  <NA> 0    0    377  <NA> 0    42  
## [136] 23   242  <NA> 323  176  104  237  414  8    NA   <NA> 569  468  331  211 
## [151] <NA> <NA> 321  372  0    383  <NA> 0    92   <NA> <NA> 0    <NA> <NA> 0   
## [166] <NA> 516  <NA> 0    <NA> <NA> 171  679  <NA> 6    NA   347  <NA> <NA> 143 
## [181] <NA> 171  <NA> 307  480  564  <NA> <NA> 0    <NA> <NA> <NA> 524  12   485 
## [196] 374  <NA> <NA> <NA> 180  8    5    <NA> 5    468  <NA> 240  <NA> <NA> <NA>
## [211] NA   <NA> <NA> 565  NA   NA   0    NA   <NA> <NA> 0    0    NA   12   0   
## [226] 603  <NA> <NA> <NA> 28   182  21   <NA> 592  411  <NA> 822  NA   NA   7   
## [241] 0    0    <NA> 0    582  912  <NA> 331  0    <NA> 9    <NA> 17   942  5   
## [256] 12   1644 NA   <NA> 0    809  386  438  <NA> 674  NA   <NA> 0    <NA> <NA>
## [271] <NA> <NA> <NA> 0    47   <NA> 0    10   <NA> <NA> <NA> NA   <NA> 0    <NA>
## [286] <NA> <NA> <NA> <NA> 22   0    <NA> <NA> <NA> 396  378  0    <NA> 692  <NA>
## [301] 406  <NA> 0    528  <NA> <NA> <NA> 6    378  126  0    0    <NA> 455  0   
## [316] 469  31   <NA> 25   23   1431 573  <NA> 459  472  6    245  183  0    <NA>
## [331] 0    <NA> 0    383  0    594  <NA> 308  642  360  131  462  390  0    449 
## [346] <NA> 0    736  <NA> <NA> NA   78   <NA> 15   0    190  NA   <NA> <NA> 400 
## [361] <NA> 379  <NA> 0    <NA> <NA> 785  0    <NA> 0    358  <NA> 369  429  0   
## [376] 475  <NA> 0    <NA> <NA> 92   99   <NA> 310  <NA> 198  463  <NA> 253  <NA>
## [391] <NA> 119  286  <NA> <NA> <NA> 0    354  338  0    0    45   465  403  576 
## [406] 0    NA   912  NA   0    383  614  741  <NA> 0   
## 159 Levels: 0 1 10 104 11 119 12 122 126 131 143 1431 15 16 1644 1674 17 ... NA
#BCR Biotab for clinical tcga

querycli_STAD<-GDCquery(project = "TCGA-STAD",
                        data.category = "Clinical",
                        data.type = "Clinical Supplement",
                        data.format = "BCR Biotab")
GDCdownload(querycli_STAD)
clinical.BCRtab.STAD <- GDCprepare(querycli_STAD)
## 
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# All available tables
names(clinical.BCRtab.STAD)
## [1] "clinical_patient_stad"        "clinical_nte_stad"           
## [3] "clinical_omf_v4.0_stad"       "clinical_radiation_stad"     
## [5] "clinical_drug_stad"           "clinical_follow_up_v1.0_stad"
# colnames from clinical_patient_stad
tibble::tibble(sort(colnames(clinical.BCRtab.STAD$clinical_patient_stad)))
## # A tibble: 63 x 1
##    `sort(colnames(clinical.BCRtab.STAD$clinical_patient_stad))`
##    <chr>                                                       
##  1 age_at_initial_pathologic_diagnosis                         
##  2 ajcc_metastasis_pathologic_pm                               
##  3 ajcc_nodes_pathologic_pn                                    
##  4 ajcc_pathologic_tumor_stage                                 
##  5 ajcc_staging_edition                                        
##  6 ajcc_tumor_pathologic_pt                                    
##  7 anatomic_neoplasm_subdivision                               
##  8 anatomic_neoplasm_subdivision_other                         
##  9 antireflux_treatment                                        
## 10 antireflux_treatment_type                                   
## # ... with 53 more rows
# pathologic tuimor stage status count
plyr::count(clinical.BCRtab.STAD$clinical_patient_stad$ajcc_pathologic_tumor_stage)   
##                   x freq
## 1     [Discrepancy]   11
## 2   [Not Available]   16
## 3    CDE_ID:3203222    1
## 4  pathologic_stage    1
## 5           Stage I    2
## 6          Stage IA   16
## 7          Stage IB   41
## 8          Stage II   33
## 9         Stage IIA   41
## 10        Stage IIB   56
## 11        Stage III    3
## 12       Stage IIIA   79
## 13       Stage IIIB   63
## 14       Stage IIIC   38
## 15         Stage IV   44
# subset for custom clinical for me

barcode<-data.frame(rse$paper_patient)
sex<-data.frame(rse$paper_Gender)
T_stage<-data.frame(rse$paper_Pathologic.T)
N_stage<-data.frame(rse$paper_Pathologic.N)
M_stage<-data.frame(rse$paper_Pathologic.M)
TCGA_sub<-data.frame(rse$paper_Molecular.Subtype)
lauren_sub<-data.frame(rse$paper_Lauren.Class)
age<-data.frame(rse$paper_Age.at.Initial.Diagnosis)
vital_sta<-data.frame(rse$paper_Vital.Status)
Days.to.Death<-data.frame(rse$paper_Days.to.Death)
Days.to.Last.Follow.up<-data.frame(rse$paper_Days.to.Last.Follow.up)
Days.to.Recurrence<-data.frame(rse$paper_Days.to.Recurrence)
ARID1A_mut<-data.frame(rse$paper_ARID1A.mutation)
KRAS_mut<-data.frame(rse$paper_KRAS.mutation)
PIK3CA_mut<-data.frame(rse$paper_PIK3CA.mutation)
RHOA_mut<-data.frame(rse$paper_RHOA.mutation)
TP53_mut<-data.frame(rse$paper_TP53.mutation)

customeclinSTAD<-cbind(barcode,
                       sex,
                       T_stage,
                       N_stage,
                       M_stage,
                       TCGA_sub,
                       lauren_sub,
                       age,
                       vital_sta,
                       Days.to.Death,
                       Days.to.Last.Follow.up,
                       Days.to.Recurrence,
                       ARID1A_mut,
                       KRAS_mut,
                       PIK3CA_mut,
                       RHOA_mut,
                       TP53_mut)
write.csv(customeclinSTAD,"custom clinical STAD ok.csv")

#from both custom clinival csv and dataFilt STAD csv, analyze using excel (best)
####subtype only TCGA tumor############
sub_TCGA<-read.csv("only tumor TCGA norm counts for graph subtype (add rse paper lauren and tcga sub).csv",sep="\t")
head(sub_TCGA)
##     Patient.ID C2orf34 FAM86A log2.CAMKMT log2.FAM86A    Q.CAMKMT    Q.FAM86A
## 1 TCGA-3M-AB46     519   1847    9.019591   10.850968 High CAMKMT High FAM86A
## 2 TCGA-3M-AB47     280    919    8.129283    9.843921                        
## 3 TCGA-B7-5816     382    943    8.577429    9.881114                        
## 4 TCGA-B7-5818     668    794    9.383704    9.632995 High CAMKMT            
## 5 TCGA-B7-A5TI     323   1041    8.335390   10.023754                        
## 6 TCGA-B7-A5TJ     707   1242    9.465566   10.278449 High CAMKMT High FAM86A
##      M.CAMKMT    M.FAM86A   T  N  M      Stage days_to_last_follow_up
## 1 High CAMKMT High FAM86A T2b N0      Stage IB                   1765
## 2  Low CAMKMT High FAM86A  T3 N2    Stage IIIB                     NA
## 3 High CAMKMT High FAM86A T4a N0 M0  Stage IIB                    812
## 4 High CAMKMT  Low FAM86A  T2 N0 M0   Stage IB                    356
## 5  Low CAMKMT High FAM86A  T4 N3 M0 Stage IIIC                    595
## 6 High CAMKMT High FAM86A T4a    M0  Stage IIB                    335
##   vital_status Mol..Sub     Lauren
## 1        Alive                    
## 2         Dead                    
## 3        Alive      MSI    Diffuse
## 4        Alive      EBV Intestinal
## 5        Alive                    
## 6        Alive
#by stage
sub_TCGA<-sub_TCGA %>% 
  mutate(Stage2 = case_when(Stage == 'Stage I' ~ 'Stage I',
                            Stage == 'Stage IA' ~ 'Stage I',
                            Stage == 'Stage IB' ~ 'Stage I',
                            Stage == 'Stage II' ~ 'Stage II',
                            Stage == 'Stage IIA' ~ 'Stage II',
                            Stage == 'Stage IIB' ~ 'Stage II',
                            Stage == 'Stage III' ~ 'Stage III',
                            Stage == 'Stage IIIA' ~ 'Stage III',
                            Stage == 'Stage IIIB' ~ 'Stage III',
                            Stage == 'Stage IIIC' ~ 'Stage III',
                            Stage == 'Stage IV' ~ 'Stage IV'))


View(sub_TCGA)
ggplot(data=subset(sub_TCGA, !is.na(Stage2)),aes(x=Stage2,y=log2.FAM86A,fill=Stage2))+
  
  
  stat_boxplot(geom ='errorbar',width=.2) +
  geom_jitter(colour='gray90',alpha=.8,width = .2)+
  geom_boxplot(width=.6)+
  theme_Publication()+
  scale_fill_aziz()+
  scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
  theme(axis.text = element_text(family = "Arial",color="black"),
        axis.title.y = element_text(vjust = 2.5),
        axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
        legend.position = 'none',
        aspect.ratio = 1.5,
        panel.grid.major.x = element_blank())+
  labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)

ggsave('FAM86A tcga by stage.svg',dpi=300, width=4,units = "in")

kruskal.test(log2.FAM86A ~ Stage2, data = sub_TCGA)
## 
##  Kruskal-Wallis rank sum test
## 
## data:  log2.FAM86A by Stage2
## Kruskal-Wallis chi-squared = 4.0519, df = 3, p-value = 0.2559
pairwise.wilcox.test(sub_TCGA$log2.FAM86A, sub_TCGA$Stage2,paired=FALSE,
                     p.adjust.method = "BH")
## 
##  Pairwise comparisons using Wilcoxon rank sum test with continuity correction 
## 
## data:  sub_TCGA$log2.FAM86A and sub_TCGA$Stage2 
## 
##           Stage I Stage II Stage III
## Stage II  0.99    -        -        
## Stage III 0.57    0.38     -        
## Stage IV  0.68    0.68     0.38     
## 
## P value adjustment method: BH
#by T
sub_TCGA<-sub_TCGA %>% 
  mutate(T2 = case_when(T == 'T1' ~ 'T1',
                        T == 'T1a' ~ 'T1',
                        T == 'T1b' ~ 'T1',
                        T == 'T2' ~ 'T2',
                        T == 'T2a' ~ 'T2',
                        T == 'T2b' ~ 'T2',
                        T == 'T3' ~ 'T3',
                        T == 'T4' ~ 'T4',
                        T == 'T4a' ~ 'T4',
                        T == 'T4b' ~ 'T4'))
ggplot(data=subset(sub_TCGA, !is.na(T2)),aes(x=T2,y=log2.FAM86A,fill=T2))+
  
  
  stat_boxplot(geom ='errorbar',width=.2) +
  geom_jitter(colour='gray90',alpha=.8,width = .2)+
  geom_boxplot(width=.6)+
  theme_Publication()+
  scale_fill_aziz()+
  scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
  theme(axis.text = element_text(family = "Arial",color="black"),
        axis.title.y = element_text(vjust = 2.5),
        axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
        legend.position = 'none',
        aspect.ratio = 1.5,
        panel.grid.major.x = element_blank())+
  labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)

ggsave('FAM86A tcga by Tstage.svg',dpi=300, width=4,units = "in")

kruskal.test(log2.FAM86A ~ Stage2, data = sub_TCGA)
## 
##  Kruskal-Wallis rank sum test
## 
## data:  log2.FAM86A by Stage2
## Kruskal-Wallis chi-squared = 4.0519, df = 3, p-value = 0.2559
pairwise.wilcox.test(sub_TCGA$log2.FAM86A, sub_TCGA$Stage2,paired=FALSE,
                     p.adjust.method = "BH")
## 
##  Pairwise comparisons using Wilcoxon rank sum test with continuity correction 
## 
## data:  sub_TCGA$log2.FAM86A and sub_TCGA$Stage2 
## 
##           Stage I Stage II Stage III
## Stage II  0.99    -        -        
## Stage III 0.57    0.38     -        
## Stage IV  0.68    0.68     0.38     
## 
## P value adjustment method: BH
#by N
sub_TCGA<-sub_TCGA %>% 
  mutate(N2 = case_when(N == 'N0' ~ 'N0',
                        N == 'N1' ~ 'N1',
                        N == 'N2' ~ 'N2',
                        N == 'N3' ~ 'N3',
                        N == 'N3a' ~ 'N3',
                        N == 'N3b' ~ 'N3'))

ggplot(data=subset(sub_TCGA, !is.na(N2)),aes(x=N2,y=log2.FAM86A,fill=N2))+
  
  
  stat_boxplot(geom ='errorbar',width=.2) +
  geom_jitter(colour='gray90',alpha=.8,width = .2)+
  geom_boxplot(width=.6)+
  theme_Publication()+
  scale_fill_aziz()+
  scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
  theme(axis.text = element_text(family = "Arial",color="black"),
        axis.title.y = element_text(vjust = 2.5),
        axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
        legend.position = 'none',
        aspect.ratio = 1.5,
        panel.grid.major.x = element_blank())+
  labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)

ggsave('FAM86A tcga by Nstage.svg',dpi=300, width=4,units = "in")

kruskal.test(log2.FAM86A ~ Stage2, data = sub_TCGA)
## 
##  Kruskal-Wallis rank sum test
## 
## data:  log2.FAM86A by Stage2
## Kruskal-Wallis chi-squared = 4.0519, df = 3, p-value = 0.2559
pairwise.wilcox.test(sub_TCGA$log2.FAM86A, sub_TCGA$Stage2,paired=FALSE,
                     p.adjust.method = "BH")
## 
##  Pairwise comparisons using Wilcoxon rank sum test with continuity correction 
## 
## data:  sub_TCGA$log2.FAM86A and sub_TCGA$Stage2 
## 
##           Stage I Stage II Stage III
## Stage II  0.99    -        -        
## Stage III 0.57    0.38     -        
## Stage IV  0.68    0.68     0.38     
## 
## P value adjustment method: BH
ggsave('FAM86A TCGA N.png',dpi=500,units = "px",width=1250)


#by M
sub_TCGA<-sub_TCGA %>% 
  mutate(M2 = case_when(M == 'M0' ~ 'M0',
                        M == 'M1' ~ 'M1'))
ggplot(data=subset(sub_TCGA, !is.na(M2)),aes(x=M2,y=log2.FAM86A,fill=M2))+
  
  
  stat_boxplot(geom ='errorbar',width=.2) +
  geom_jitter(colour='gray90',alpha=.8,width = .2)+
  geom_boxplot(width=.6)+
  theme_Publication()+
  scale_fill_aziz()+
  scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
  theme(axis.text = element_text(family = "Arial",color="black"),
        axis.title.y = element_text(vjust = 2.5),
        axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
        legend.position = 'none',
        aspect.ratio = 1.85,
        panel.grid.major.x = element_blank())+
  labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)

ggsave('FAM86A tcga by Mstage.svg',dpi=300, width=4,units = "in")

ggsave('FAM86A TCGA M.png',dpi=500,width = 1400,height = 1734,units = "px")

#save edited csv
write.csv(sub_TCGA,"subtype TCGA STAD plot subtypes.csv")



#statistic subtypes kruskal wallis
kruskal.test(log2.FAM86A ~ Stage2, data = sub_TCGA)
## 
##  Kruskal-Wallis rank sum test
## 
## data:  log2.FAM86A by Stage2
## Kruskal-Wallis chi-squared = 4.0519, df = 3, p-value = 0.2559
kruskal.test(log2.FAM86A ~ T2, data = sub_TCGA)
## 
##  Kruskal-Wallis rank sum test
## 
## data:  log2.FAM86A by T2
## Kruskal-Wallis chi-squared = 0.073071, df = 3, p-value = 0.9949
kruskal.test(log2.FAM86A ~ N2, data = sub_TCGA)
## 
##  Kruskal-Wallis rank sum test
## 
## data:  log2.FAM86A by N2
## Kruskal-Wallis chi-squared = 1.3156, df = 3, p-value = 0.7254
wilcox.test(log2.FAM86A ~ M2, data = sub_TCGA)
## 
##  Wilcoxon rank sum test with continuity correction
## 
## data:  log2.FAM86A by M2
## W = 4209.5, p-value = 0.1924
## alternative hypothesis: true location shift is not equal to 0
#addition subtype based on rse paper
#lauren
sub_rse<-read.csv("only tumor TCGA norm counts for graph subtype (add rse paper lauren and tcga sub).csv",sep='\t')
head(sub_rse)
##     Patient.ID C2orf34 FAM86A log2.CAMKMT log2.FAM86A    Q.CAMKMT    Q.FAM86A
## 1 TCGA-3M-AB46     519   1847    9.019591   10.850968 High CAMKMT High FAM86A
## 2 TCGA-3M-AB47     280    919    8.129283    9.843921                        
## 3 TCGA-B7-5816     382    943    8.577429    9.881114                        
## 4 TCGA-B7-5818     668    794    9.383704    9.632995 High CAMKMT            
## 5 TCGA-B7-A5TI     323   1041    8.335390   10.023754                        
## 6 TCGA-B7-A5TJ     707   1242    9.465566   10.278449 High CAMKMT High FAM86A
##      M.CAMKMT    M.FAM86A   T  N  M      Stage days_to_last_follow_up
## 1 High CAMKMT High FAM86A T2b N0      Stage IB                   1765
## 2  Low CAMKMT High FAM86A  T3 N2    Stage IIIB                     NA
## 3 High CAMKMT High FAM86A T4a N0 M0  Stage IIB                    812
## 4 High CAMKMT  Low FAM86A  T2 N0 M0   Stage IB                    356
## 5  Low CAMKMT High FAM86A  T4 N3 M0 Stage IIIC                    595
## 6 High CAMKMT High FAM86A T4a    M0  Stage IIB                    335
##   vital_status Mol..Sub     Lauren
## 1        Alive                    
## 2         Dead                    
## 3        Alive      MSI    Diffuse
## 4        Alive      EBV Intestinal
## 5        Alive                    
## 6        Alive
sub_rse<-sub_rse %>% 
  mutate(Lauren2 = case_when(Lauren == 'Diffuse' ~ 'Diffuse',
                             Lauren == 'Intestinal' ~ 'Intestinal',
                             Lauren == 'Mixed' ~ 'Mixed'))

ggplot(data=subset(sub_rse, !is.na(Lauren2)),aes(x=Lauren2,y=log2.FAM86A,fill=Lauren2))+
  
  
  stat_boxplot(geom ='errorbar',width=.2) +
  geom_jitter(colour='gray90',alpha=.8,width = .2)+
  geom_boxplot(width=.6)+
  theme_Publication()+
  scale_fill_aziz()+
  scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
  theme(axis.text = element_text(family = "Arial",color="black"),
        axis.title.y = element_text(vjust = 2.5),
        axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
        legend.position = 'none',
        aspect.ratio = 1.85,
        panel.grid.major.x = element_blank())+
  labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)

ggsave('FAM86A tcga by Lauren.svg',dpi=300, width=4,units = "in")


ggsave('FAM86A TCGA Lauren2.png',dpi=500,width = 1500,units = "px")

kruskal.test(log2.FAM86A ~ Lauren2, data = sub_rse)
## 
##  Kruskal-Wallis rank sum test
## 
## data:  log2.FAM86A by Lauren2
## Kruskal-Wallis chi-squared = 11.864, df = 2, p-value = 0.002653
pairwise.wilcox.test(sub_rse$log2.FAM86A, sub_rse$Lauren2,
                     p.adjust.method = "BH")
## 
##  Pairwise comparisons using Wilcoxon rank sum test with continuity correction 
## 
## data:  sub_rse$log2.FAM86A and sub_rse$Lauren2 
## 
##            Diffuse Intestinal
## Intestinal 0.0016  -         
## Mixed      0.4017  0.4017    
## 
## P value adjustment method: BH
#Mol.sub
colnames(sub_rse)[16] #"Mol..Sub"
## [1] "Mol..Sub"
sub_rse<-sub_rse %>% 
  mutate(mol_tcga = case_when(Mol..Sub == 'CIN' ~ 'CIN',
                              Mol..Sub == 'EBV' ~ 'EBV',
                              Mol..Sub == 'GS' ~ 'GS',
                              Mol..Sub == 'MSI' ~ 'MSI'))

ggplot(data=subset(sub_rse, !is.na(mol_tcga)),aes(x=mol_tcga,y=log2.FAM86A,fill=mol_tcga))+
  
  
  stat_boxplot(geom ='errorbar',width=.2) +
  geom_jitter(colour='gray90',alpha=.8,width = .2)+
  geom_boxplot(width=.6)+
  theme_Publication()+
  scale_fill_aziz()+
  scale_y_continuous(expand=expand_scale(mult = c(0.1,0.2)))+
  theme(axis.text = element_text(family = "Arial",color="black"),
        axis.title.y = element_text(vjust = 2.5),
        axis.text.x = element_text(angle = 45,vjust = 1, hjust=1),
        legend.position = 'none',
        aspect.ratio = 1.5,
        panel.grid.major.x = element_blank())+
  labs(y=expression('FAM86A expression (log'[2]*")"),x=NULL)

ggsave('FAM86A tcga by mol_tcga.svg',dpi=300, width=4,units = "in")

kruskal.test(log2.FAM86A ~ mol_tcga, data = sub_rse)
## 
##  Kruskal-Wallis rank sum test
## 
## data:  log2.FAM86A by mol_tcga
## Kruskal-Wallis chi-squared = 19.22, df = 3, p-value = 0.0002462
pairwise.wilcox.test(sub_rse$log2.FAM86A, sub_rse$mol_tcga,paired=FALSE,
                     p.adjust.method = "BH")
## 
##  Pairwise comparisons using Wilcoxon rank sum test with continuity correction 
## 
## data:  sub_rse$log2.FAM86A and sub_rse$mol_tcga 
## 
##     CIN     EBV     GS     
## EBV 0.04036 -       -      
## GS  0.02782 0.57278 -      
## MSI 0.22058 0.00258 0.00011
## 
## P value adjustment method: BH
ggsave('FAM86A TCGA sub tcga.png',dpi=500,width = 1250,units = "px")